Doctor Who: The Equestrian Chronicles
by The TARDIS Courier
Summary: After an unknown event in our universe, The Doctor must now learn to live in world where Ponies are the dominant species, will he find a way back or will he settle down and make a life in this new world...hell no!, who can resist a time travelling pony, cue the music. LunaXOC
1. Episode 1 Part 1 Pilot

COURIER: hi guys here is a rewritten version of episode one as a two partner, I think I've sorted the grammar but please tell me if anything major is wrong because if not this is going on FiMFiction.

Disclaimer: I own nothing…NOTHING, apart from Dr Junior

Doctor Who:

Equestrian Chronicles

**Ep 01: PART ONE**

_What the hell am I! What the hell am I!_

It was a peaceful day in the land of Equestria, and no area was more happy than ponyville, there were many ponies who lived here but one was about to get a massive surprise.

"Oh, Spike I don't understand, why is the princess not doing anything. The mare on the moon will return tomorrow and she wants me to make friends!" the voice in distress was a young purple unicorn by the name of Twilight Sparkle, the personal student of Princess Celestia, the ruler of Equestria, next to the purple mare was a little purple dragon, reading a comic book, relaxing unlike his pony friend.

"Come on twilight, maybe it really is an old ponytale but you still have some tasks, so my advice is ill help you get those done and then you can return to your research" Twilight looked at her dragon, with shock in her eyes.

"Wow, spike I didn't know you could think like that, I thought food was all you thought about" she commented surprised by her friends use of his usually one sided mind

"and that" the mare rolled her eyes and was about to walk out the door when a strange sound could be heard, Twilight could not put her hoof on it yet to her it sounded like, Pain.

*VVROOPP VVRROOP VVRRROOPP VROOP CRAAAASH!*

"What was that!?" twilight exclaimed after the thunderous crash

"It landed in the west wing, come on spike" spike was terrified and wanted to run, yet he knew his owner would say differently.

"Don't you run away from things like this" twilight shot a glare at the purple dragon to which he followed the mare into the west wing of the library. "What is that?"

"I don't know seems familiar" to what spike was referring to was a large blue wooden box, that twilight thought that she had seen before, on the box was writing at the top (despite it being on its side) "police public call box, wonder what it is?" then as if on cue the doors swung open and out came a grey Pegasus with a crazy messed up mane and wearing ripped clothes that clearly did not fit anyway, the only item which seemed to be undamaged was a tartan tie tied loosely around his neck. Exiting the box, he tried to stand on his hind legs and attempted to wipe blood off his face not realising his hands where covered in more blood than his face, like he had just survived a slaughter or committed one, despite his appearance, he had a big grin on his face.

"sweet, a unicorn, never seen one before" the Pegasus was staring at twilight like she was some specimen, being observed, till he spotted spike "oh hold on, is that... no way A DRAGON!" and like a foul on his birthday began jumping up and down with joy...before falling on his stomach since he lost his balance, standing on his hind legs "ow, what the?, why did I fall over?" getting up he noticed his hooves and began to question his body "wait hold on, why do i have hooves?, AHHHHHH!, I'm a horse!, NOOOOOOOO!" Twilight was tired of his nonsense and began to try and get some answers.

"Would you stop and tell me who you are?" the strange pony stopped freaking and stared wide eyed at twilight.

"YOU CAN TALK!, THE f**K" he began freaking out again this time moving away from twilight, like we was staring at a monster "WHAT THE HELL IS GOING ON!" he then looked at his hooves then back at twilight with fear in his eyes _"what the hell am I"_ then as his voice lowered he collapsed unconscious followed, by golden vapour exiting his mouth. Twilight was shocked to say the least never had any pony reacted to anything like that before, spike however was still trembling.

"Twilight, what just happened?" the mare looked at her small friend and back to the supposed insane Pegasus lying on the floor.

"I don't know spike, but I say we wait for him to wake up, then get some answers from him" knowing that this pony was far too heavy for both twilight to lift, she decided to use her magic to teleport him to the couch. Placing a blanket and pillows by him to make him comfortable twilight sat there staring at the crazy pony, who reacted like he had no idea who he was, and the fear in his eyes, it was worse than a frightened foul on nightmare night.

"_What the hell am I?" _Those words rung in her head, for what seemed like hours, not knowing what to do.

"_Maybe I should call princess Celestia...no I need to get some answers first" _after calming down spike both dragon and mare, left to complete the errands she was told to do.

**Sometime later**

Twilight returned to find her guest exactly where she'd left him, EXACTLY, he hadn't moved an inch. Sitting in front of him again, with her suspicion turning to concern, spike on the other hand had hoped in his bed for a nap, since he was still just a baby.

"maybe we should call a doctor what if he's ill" then the moment she finished, the Pegasus's eyes shot opened and he got up and looked around, scanning the area, finally his eyes resting on the purple mare in front of him.

"Did you call?" to twilights surprise he had the smile he had when he first exited his box, yet this time he was cleaned up and...

"_His wounds they healed up! not a scratch on him" _she thought, unsure who this pony was

"What's your name?" this pony was really strange first he freaks out about the most basic of things next the second he is conscience, he is asking personal questions.

"I'm Twilight, Twilight Sparkle" she answered him proudly.

"Well may I say that, that is a beautiful name, don't believe I've heard it before" though she would deny it she was blushing from his complement, no pony had ever commented on her name before.

"Well thanks, may i ask what is yours?" the pony gave a cheerful smirk, like he knew what was coming next.

"I'm The Doctor" twilight had cocked her head what an odd name, yet she believed that it was just his title.

"Doctor Who?" she asked thinking she didn't hear him correctly.

"Just that, The Doctor, I know it's confusing but I'm been going by that for centuries" he was beginning to show the craziness he had displayed before.

"oookkkaaaayyy, you're not going to freak out again are you?" the doctors eyes widened, not as much as they did last time, in fact he looked confused .

"What? Oh! No, no need to worry that was just a sever culture shock, I mean what would you do if your dragon over there could talk, ha-ha" he said with a chuckle not realising that Spike could indeed talk.

"He can" Spike said annoyed at the grey Pegasus.

"Oh snap, can all animals talk, or is it just horses and dragons" he said again surprised at a talking animal but unlike last time he didn't freak out about it.

"Pony, and no quite a few animals can talk, but they way you reacted, it was like you had no idea, who you were" on her statement, the doctor began looking around his body inspecting it.

"that because I didn't, I wasn't a horse last time a checked" twilight had noticed he kept saying the word horses, when pony is the correct term it seemed he was going to be a annoyance on that.

"Pony, you're a ..." before she could finish her sentence the doctor screamed like he did when he first saw Spike.

"Pegasus! I HAVE WINGS! AWSOME! And what's this, a tattoo? Interesting never had a tattoo before" he exclaimed jumping up and down, a bit like pinkie when she gets excited before staring at his flank.

"That's your cutie mark" the doctor had his confused face again, only this time he cocked his head.

"Come again?"Twilight turned around to show the doctor her cutie mark, which was 5 small stars, around a larger pink star, which was pictured sparkling.

"Your cutie mark, it's a sign to show what your talent is" she said lowering her flank.

"Well yours seems to match you well, sparkle by name and by talent" again a blushing twilight turned her head in embarrassment.

"yeah, I guess so" The Doctor got up, with some difficulty and attempted to open his wings to stretch which to her amazement, was a very impressive wing span almost the size of Celestia's wings " sweet Celestia" The Doctor looked at Twilight again with confusion.

"Who?" It was now her turn to be confused, no pony had not heard of Princess Celestia.

"You don't know who Celestia is" despite the seriousness for twilight, The Doctor didn't seem to care.

"Nope, but I'm sure to find out later on, now what's up?" he said now concentrating on Twilight's reaction.

"What?" the doctor rolled his eyes like he had seen the same thing over and over and was getting tired of it.

"Humans, horses, there's no difference! You said Celestia, when i stretched my wings, what about?" he raised his voice irritated for a bit before calming and tell Twilight about what he was going on about.

"Ohh! It's you have an impressive wing span, I've only seen one other pony to have a wing span that big" this seemed to tickle the doctors fancy as he didn't know he had such unique wings.

"Who?" He asked curiously

"Well...Princess Celestia's actually" The Doctor raise an eyebrow and brought his hoof to his chin.

"Well, going by your reaction to my wings, and the fact that this Celestia is a princess; I'm guessing she is your ruler" Twilight nodded to confirm.

"And my mentor" The Doctor was again confused but decided to save it for another day. "One more thing your cutie mark, can I have a look at it"

"yea sure" The Doctor replied cheerfully, turning to show twilight the mark on his flank "not had a good look at it myself to be honest" upon looking at his cutie mark, Twilight had no idea what it was for, the mark in question was a galaxy. "a galaxy huh, i was expecting an hourglass, or a clock"

"Well, what is your talent" The Doctor again put his hoof to his chin and began to think.

"Well, I myself expected time to be my talent, but now i think about it, time has nothing to do with it" Twilight was reconsidering the insane pony idea.

"What are you talking about?" she asked The Doctor now getting sick of him not making any sense.

"well, miss sparkle, the box I came out of is a time machine/spaceship and I know it sounds crazy, but she is rebuilding so you're going to have to wait, anyway my ship can go anywhere in the universe to any point in existence, but time is doesn't exist, it just what we use to keep a record of said existence, my talent isn't time fabrication but the ability to travel anywhere, any when in the cosmos I wish. That should sum it up" The Doctor explained this in about 30 seconds but Twilight seemed to be able to keep up with him, barley.

"Wow that actually made a lot of sense doctor" The Doctor then jumped up and landed on his four new hooves and attempted to walk "please don't tell me you don't know how to walk?" The Doctor had a frown on his face as he tried to get his legs to move the correct way.

"Like I said, I'm new to being a horse, not less than a day ago I was bipedal, now I'm a horse on all fours, plus I'm hungry" he revealed with a gurgling stomach in-between his explanation.

"Ok, I'll help you walk and get you something, in return you give me some answers, deal?" She offered getting up and heading for the kitchen.

"On the food, deal, on the walking, no I've got it, it's just like crawling, only I haven't crawled, in over 400 years" he said revealing his age casually.

"Oh ok...WAIT! Did you say 400 years!" The Doctor looked at the shocked twilight, realising he should explain that feature.

"ahh, yea, might as well say I'm 462 years old" after Twilight calmed down, she made a few sandwiches and sat down next to The Doctor, ready to listen.

"Ok explain the basics" The Doctor cleared his throat after taking a bite of his hay sandwich.

"ok, my name is the doctor, I'm an alien to you, called a time lord, that box in the other room in my home/ space-time ship, called a TARDIS, which stands for Time And Relative Dimensions In Space, time lords are a race of, I would say humanoid, but it won't mean anything, anyway they are aliens who have, unlocked the ability to travel in time and space, since they live near temporal technology their live span became extremely long considering 100 years as being a child, but to top of the life span, we time lords have the unique, ability to change our appearance upon fatal damage to our bodies and so we change our physical appearance, the process is random and in result I have been turned into a Horse..." half way through his very long explanation Twilight had corrected him when he said horse instead of pony.

"Pony" The Doctor gave Twilight a look and decided to role with it.

"Pony, instead of the common bipedal-humanoid shape, so I have absolute no experience, as a...pony what so ever and it seems I am in a different world to my own as I have no knowledge of your history, and cultures. There done, any questions?" Twilight listened as best she could and now knew a bit about him be it not much.

"Actually, just one so far" she said calmly despite everything she had heard.

"What?" he said finishing off his sandwich.

"How did you eat, those sandwiches without stopping your explanation?" she asked pointing at the empty plate.

"I ate the first one, a bit the second and stuffed the last two in my jacket pocket for later, the one I was eating well, I'm a time traveller I probably stole it off myself in the future, speaking of its nearly sunrise, isn't there a party, thing going on" he said motioning to the window which viewed the moon slowly setting.

"Yea, the summer sun festival, when Celestia raises the sun for the longest day of the year, how did you know?" she asked wondering who he knew important events yet never being here before.

"well I read that book on rulers of Equestria, guessed it was what this place was called, and it said something about Princess Celestia's ability to raise the sun and moon, and well a galaxy is a celestial body, to I can tell the time of day, the weather forecast and the position of the sun in your solar system, by the way Celestia probably doesn't raise the sun, but instead turns the planet to face the sun" he said with a little smile on his face, he seemed really interested in the workings of Equestria.

"Wow, you are really smart" The Doctor gave a cocky smirk.

"I dabble, now this is a once a year event I would very much like to see it" Twilight was actually Glad she had made a friend like Celestia had asked, and with is knowledge, he might teach her a few things that even Celestia may not know.

"Sure, let me just wake up spike" The Doctor jumped of the couch on to the floor and continued to the front door.

"Don't bother, he got up and left a few minutes ago, when you were in the kitchen, I said we'd catch up later" he explained while getting up.

"you do think ahead" both ponies walked out of Twilights house and walked towards the stage that the ceremony would take place, both would continue to chat about different topics Twilight giving of a few giggles when The Doctor almost trips over. After ten minutes of walking The Doctor and Twilight walked to the crowd looking up at another chestnut coloured pony "that's the mayor, mayor mare" while walking Twilight told The Doctor about several ponies he need to know about.

"Wait, mayor...mare as in female hors...uhh, pony" he said with confusion almost forgetting to use the proper term.

"yea, believe it or not, I've not been here long, in fact I arrived today" The Doctor could tell that his new friend was happy as well as everyone else, but he felt something...off, looking up he saw the moon and several stars which moved closer behind the moon.

"Dam it!" Twilight saw something was off about The Doctor, in such a short amount of time he seemed, more serious.

"Doctor, what's wrong?" The Doctor turned to his purple equine friend.

"That book I read, it mentioned another mare that ruled Equestria and I think you knew already" that's when it hit Twilight like a hammer on her horn.

"The mare on the moon, how did I forget?" she yelled but over the mass of chatting ponies she wasn't heard.

"It was my fault, my arrival must have taken your mind off it" twilight was worried, till she realised that The Doctor actually believed in the mare on the moon.

"Wait you believe in the story" The Doctor had a serious look on his face that Twilight never knew he had due to his clumsy looking personality.

"in all my years, I have learned one thing about fairytales..." and if on cue the shocked reaction showed, something was not right "...and it's that they are always, always truth behind them" following his final words was purple smoke flooded the stage and formed a Beautiful mare in dark armour, with a coat as black as the void, despite her intimidating look, she was slim and elegant.

"Oh, my beloved subjects, it's been so long since I've seen you small little sun loving faces" fear had stricken everyone/pony, yet there was one certain rainbow coloured pony, was a bit too bold.

"What did you do with our princess?" Rainbow Dash shouted, being held back by the tail by Apple Jack.

"Hahaha, why am I not royal enough for you?" this dark mare was definitely the definition of the over the top bad guy, yet her mood was like lighting "don't you know who I am" Like a growing itch, another pony started commenting, a bright pink one to be precise.

"Ohh Ohh, more guessing games, uhh, hokey smokes, how about Queen Meanie, no! Black snootie, Black snoot..." Pinkie Pie that was known to never shut up was silenced by Apple Jack with an apple while who was still holding Rainbow Dash back. Yet the dark mare didn't pay any attention to her focusing on herself.

"Does my crown no longer count, know that I have been imprisoned for 1000 years" Twilight was getting agitated, seeing this evil mare terrorise innocent ponies no apparent reason.

"I have to do something" she began walking towards her, yet The Doctor stopped her remembering what someone had said to him, that no matter where he goes trouble will find him.

"No I will, I have experience in this sort of thing" he said coldly, not knowing much about how this world works he didn't want any harm to come to his new friend

"But you'll get hurt" Twilight had a vague idea of how dangerous this mare was but she didn't know him

"No I won't...trust me, I'm The Doctor" reassuring Twilight with his cocky smirk he walked through the crowd to face his new adversary

"Did you not recall the legend, did you not see the signs" out of the group of ponies one grey coloured Pegasus walked out, to confront her with a dark yet warm look in his eyes.

"I did and I know who you are, mare on the moon or better yet...Nightmare Moon" the fact this random pony had knowledge of the dark mare made most ponies gasp, as nightmare moon is, the fabled mare of nightmare night (Halloween).

"Well, well, well somepony who remembers me, so you know why I'm here" her movements and voice tone would scare a pony, but Nightmare Moon wasn't talking to a pony.

"yea, yea, yea you're here to bring eternal darkness and rule all of blah, blah, blah" The Doctor seemed to be treating this like a game, a game he played before, yet unlike his ruthless opponent he was one to show compassion "but I know what it's like to live alone for a long time, let me help you, this is not what you're meant to do" this seemed to strike a chord in the mare of shadows.

"You know nothing, and this is what I'm DESTINED to do, remember this day little ponies for it was you last, from this day forth the night shall last FOREVER!" every pony plus one dragon was frightened to the bone with the exception of the brave Rainbow and Time Lord.

**Next time on DW: EQUESTRIAN CRHONICLES**

What's an element of harmony?


	2. Episode 1 Part 1 Pilot 2 conclusion

COURIER: ok, episode 1 part 2 this is the part with the most grammar errors I could see but hope you enjoy it all the same.

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Who:

Equestrian Chronicles

**Ep 01: PART TWO**

_What's an element of harmony?_

_**Last time on**_

_**The Equestrian Chronicles**_

"_Oh, my beloved subjects, it's been so long since I've seen you small little sun loving faces" fear had stricken everyone/pony at Nightmares sharp voice._

"_Ohh, Ohh, more guessing games, uhh, hokey smokes, how about Queen Meanie, no! Black snooty, Black snoot..." Pinkie Pie said making a game out of the situation._

"_I have to do something" she began walking towards her, yet The Doctor stopped her remembering what someone had said to him, that no matter where he goes trouble will find him._

"_No I will, I have experience in this sort of thing" he said coldly, not knowing much about how this world works he didn't want any harm to come to his new friend._

"_But you'll get hurt" Twilight had a vague idea of how dangerous this mare was but she didn't know him._

"_No I won't...trust me, I'm The Doctor" reassuring Twilight with his cocky smirk he walked through the crowd to face his new adversary._

**Now the conclusion**

"Well, well, well somepony who remembers me, so you know why I'm here" her movements and voice tone would scare a pony, but Nightmare Moon wasn't talking to a pony.

"yea, yea, yea you're here to bring eternal darkness and rule all of blah, blah, blah" The Doctor seemed to be treating this like a game, a game he played before, yet unlike his ruthless opponent he was one to show compassion "but I know what it's like to live alone for a long time, let me help you, this is not what you're meant to do" this seemed to strike a chord in the mare of shadows.

"You know nothing, and this is what I'm DESTINED to do, remember this day little ponies for it was you last, from this day forth the night shall last FOREVER!" Nightmare cackled accompanied with lightning.

"then you leave me no choice" The Doctor had played this card far too often than he liked and knew he would have to stop her, yet the mayor and the royal guard had other plans.

"Seize her! Only she knows where the princess is!" the royal guard attempted to arrest Nightmare moon, but they should have known she was far too powerful.

"Stand back! You fools!" after repelling her attackers, she fled to who knows where, yet with the now free Rainbow Dash on her tail. Twilight walked to the brave stallion who had watched his new foe escape.

"Doctor what are you going go after her!"

"As much as I would want to, I can't, I don't know how to fly. But we need to stop her, come on let's get back to the library I need my screwdriver" with both Pegasus and unicorn running to the library, overlooking them was Rainbow Dash who fail to catch up to Nightmare moon in time.

"Where are you two going?" she said suspicious of the grey Pegasus

**LATER AT THE LIBRARY**

Spike who was found unconscious by Twilight lay in his bed, waking up only to fall asleep, after telling them to stop Nightmare no matter the cost.

"poor guy, his heart is in the right place, shame he is just a baby" The Doctor who still couldn't figure how to pick up his sonic screwdriver with a hoof, decided to ignore the logic and accept the impossible, and to his amazement he actually picked it up "but how, i have no bloody fingers!, what the F**k logic" as soon as he started questioning it the screwdriver fell "ok, ok, screw logic" he stated before picking it up again and putting it in his jacket pocket which he now had on, unlike his tie his leather jacket was damage but it had to do since he had no pockets, The Doctor was ready to stop Nightmare Moon, Twilight on the other hand.

*CRASH*

"Where is it, elements, elements how can I stop nightmare moon without the elements" she was tossing and turning every book she had with no avail.

"Twilight, as much as I love books, I don't think the location of anything as powerful as these elements of harmony would be in your average library book" and as if lightning its self was present Rainbow dash shot into the library and was right up in The Doctor's face.

"And just what are the elements of harmony! And how did you know about Nightmare Moon huh, you a spy?" The Doctor unfazed by the multi-coloured Pony didn't back down from Rainbows aggressive approach and stated walking towards her forcing her to move backwards, with the same force she used on him.

"We are in a library, you figure out how I know about a Power hungry horse, pony whatever, who is only ever mentioned in Fairy tales!" and with all his knowledge he still had to learn a few things, with Twilight happy to help.

"Doctor, their called ponytales" The Doctor raised an eyebrow then walked of cursing in another language. Just behind rainbow dash was Apple Jack who had just entered the library.

"Simmer down sally, RD he ain't no spy, but both of them sure know what's going on, dont'cha twilight and…" The Doctor rolled his eyes at the continued question of in his life

"Doctor" he said quickly and annoyingly

"Doctor wh..." Apple Jack was about to finish her question but was interrupted by a irritated Time Lord

"Just the doctor" not only was Rainbow and Apple jack here but other ponies that Twilight knew has also arrived "friends of yours Miss Sparkle"

"Um yea, Doctor this is Apple Jack, Fluttershy, Rainbow Dash, Rarity and Pinkie Pie" Twilight gave The Doctor the names of her new friends while every Pony greeted the Doctor in their own way, after the quick introduction, The Doctor decided to get straight down to business.

"Now , you want to help, fine glad to accept, but first I'm not familiar with a few things you find simple for example I'm older than all of you combined and I can't fly" this statement made Rainbow, giggle at how a fully grown Pegasus can't fly "anyway, I have just read, about these legends out of one book, Twilight here is the one who did most of the research, I also confronted Nightmare Moon as I have had past encounters in similar situations...minus the walking on all fours, these artifacts known as the Elements Of Harmony sound incredibly powerful and are the only thing that could stop her without causing lasting damage"

"What is that suppose ta mean" Apple Jack asked with a very strong accent which sounded like Texan.

"It means using the elements will stop her without killing her but I'm not taking chances, if the planet stays without the sun for too long, Equestria will die" the six mares could see the seriousness in his eyes and knew what he was saying was the truth.

"So we need to find out where the elements are and what they do" Twilight stated with concern till Pinkie burst the bubble in a good way.

"Elements of harmony, a reference guide" she read out, like it was hiding in plane site, contradicting The Doctor's previous statement.

"Ignore my statement, about powerful things in average books, seems everything logical in this world is irrelevant" he said before bagging his head on the wall.

"How did you find that" Twilight stated in disbelieve

"It was under E" replied Pinkie jumping up and down while The Doctor stood there gobsmacked

"Figures" he said to himself mentally face palmed/ hoof smacked himself, Twilight then pulled the book out and opened it, The Doctor walking up behind her reading the page aloud

"There are 7 elements of harmony, but only six are known kindness, laughter, generosity, honesty, loyalty and trust, the 6th is a mystery, blah, blah, blah, here we go the last known location of the elements was the original castle of the royal sisters, which resides in ...

**Jump 10 minutes, to the entrance to the everfree forest**

"_**The everfree forest**_" was everyone's (I'm going to go by human speech, I'm the narrator after all) reaction to the location of the castle, apart from Twilight and The Doctor.

"Apparently, Celestia chooses towns randomly" The Doctor mentioned calmly.

"Yes a different town, every year" Twilight confirmed.

"Then why do I feel like she didn't choose ponyville for its atmosphere, but for the fact that it happens to be right next to the castle, that this all started from" The Doctor had thought about this carefully, this Celestia seemed to be a great planner.

"Wee, let's go!" was Pinkies reaction, which continued to confuse The Doctor more than the hoof impossibility; no one alive is this energetic.

"Not so fast, look I appreciate the offer, but i really would rather do this on my own" Twilight was tightly focused on stopping Nightmare moon, which made The Doctor think about his past, he had always told people to wait for him to sort it, only to have them taken away.

"_No more"_ was the word his father had said the last time they met during the war.

"No can do sugar cube, we ain't going to let any friend of ours go into that creepy place alone" if The Doctor learned anything so far was that no matter what you do, Apple Jack could counter anything, yet the thought of friends made Twilight queasy, The Doctor could tell she didn't have many friends before today "we're sticking to you like caramel on a candy apple" a cold shiver fell down The Doctor's back and out his through wings.

"I sense a long future of apple related puns with you Apple Jack, don't I" he said before Apple Jack walked straight into the forest with the rest of the group leaving Twilight, The Doctor and pinkie who was also beginning to follow the group.

"Especially if there are actually candy apples in there" The Doctor and Twilight looked at pinkie with a blank expression "what those things are good"

"Twilight, something is bothering you, what is it?" The Doctor asked looking straight into the forest with the uneasy Twilight standing next to him.

"I'm just not used to having…friends" Hesitant to use the word flung around ponyville like currency.

"trust me you'll get used to it and you'll enjoy every minute you spend with them…400 years of travelling and I treasure my friend above even the brightest of stars" he reassured Twilight giving her hope for the future.

"Thanks Doctor, now let's go and save Equestria" yelling at the top of her lungs, motivated by The Doctors speech

"Avanti" The Doctor said to himself before following his brand new group of friends

**5 minutes later**

The six girls of the group, as only one boy was there, where all creeped out by the forest as it didn't look like it had been maintained in years.

"So none of you have actually been in here before" was Twilights attempt to break the ice.

"Oh, heavens no, just look at, it's dreadful" Rarity replied with her true lady like voice

"And it ain't natural, folk say it don't work the same as Equestria" Apple Jack added to the conversation with a chill from her spine

"Looks natural to me, in fact it's the most familiar thing I've seen since I got here, it just looks like the common forest in England minus the bad weather" The Doctor was the only pony actually admiring the forest as it reminds him of the many forests in his universe.

"Noooo poooony knooows, you know why?" Rainbow tried to scare everyone yet only half worked.

"Rainbow, quit it" Apple Jack tried to defend her friends, but she knew rainbow all too well.

"because every pony that has ever come in has never come OUT!" and on that note the ground cave in and all but Rainbow and Fluttershy fell, thanks to Docs inability to fly he decided to use his large wings to glide to safety, Pinkie and Rarity were caught by Rainbow and Fluttershy while Apple Jack caught a branch and Twilight hung by the edge, apple let go of the branch and tried to help Twilight.

"Let go" Apple told Twilight to let go as calmly as possible only to be bit back by the panicking Twilight.

"Are you crazy?" she screamed followed by a bit of the cliff breaking off.

"No I ain't I promise you'll be safe" Apple Jack was doing her best to reassure Twilight but it didn't have much effect.

"That's not true" still in a state of panic The Doctor Tried to steer himself towards Twilight to tell her she was going to be safe but instead he fell to the ground.

"Uh-oh, ahhhh!" he screamed as he fell

"now you listen here what I am telling you is the honest truth, let go and you'll be safe" now beginning to trust her as Apple Jack didn't seem the lying type, Twilight let go to fall several feet, then she was caught by both Rainbow and Fluttershy, with every one down safely, Apple Jack using her own skills to get down, and the doctor falling several feet and being the only one to take the full fall, slammed front firt on the ground making it crack from the force

"Oww, everyone...ponies alright" The Doctor asked getting a nod from everyone and a smile from Twilight. Later on while all six ponies plus one Time Lord continued their quest Rainbow Dash was busy bragging about saving everyone except The Doctor who had a bandage on his head.

"Catching you in the nick, of time" Rainbow said finishing her glorified retelling of the event.

"Leaving me to fall to my doom, I told you I couldn't fly!" The Doctor shouting at Rainbow, both giving each other a evil glare.

"Yes Rainbow I was there, and I'm very grateful but we gotta..." cutting Twilight off was a large beast that seemed to catch The Doctor's eye

"A MANTICOR! I am one lucky guy!" The Doctor screamed like a little school filly jumping around at the sight of the beautiful creature, yet Twilight only saw it as an obstacle.

"We need to get past it" she declared motivating the others to take battle positions.

With every one trying to put it down and failing at it, The Doctor was too mesmerised by the creature and Fluttershy saw something was wrong but was too...well shy to say anything.

"Wait…WAIT!" everyone stopped at the unlikely event of Fluttershy speaking up, The Doctor now out of his trance could see the issue the beast was having. Walking back to the group, turned out that a thorn was stuck in his hand.

"How did you know that the thorn was in his hand?" The Doctor asked while returning to the group.

"I didn't, sometimes you have to show a little kindness" Twilight had heard her answer to the doctor question, but The Doctor himself did his thinking pose when he brought his hoof to his chin.

"Hmmm, honesty and kindness, Doc you are a genius" later on the girls plus The Doc, stumbled into a darker part of the forest.

"my eyes need a rest from this icky forest..." Rarity complained in her posh accent only to have darkness cover everything as if on her command "...didn't mean it that literal" after some minor arguments about pushing and shoving, the girls began to scream at the trees, which for some reason made scary faces, The Doctor who was completely disorientated by the sudden light from Twilights horn and the screaming, once he could focus again he saw that the girls were scared of trees which did look a bit weird, he would of hoof slapped himself if not for that pink pony laughing her face off.

"Pinkie run!" Twilight told her to back away, before she started... "Tell me she's not"

"She is" it seemed all the girls knew what she was doing so I'll see you in a few.

_**Intermission**_

Well, all the girls are laughing and The Doctor, just didn't get it.

"I don't get it there just trees..." -_- "well at least that's laughter done, 3 down 3 to go" coming to a river the team discover that there is no bridge.

"How are we going to get across?" Twilight asked.

"Hold on do I hear crying" The Doctor was right, over to the left was a crying sea serpent with half his moustache gone "ohh wow you my friend you look stunning" was The Doctors reaction to the crying sea snake till he noticed have his moustache was gone. "uh, minus the tash"

"Excuse me, why are you crying" Twilight asked the serpent.

"well, I was minding my own business when, some purple smoke, zoomed past and cut half of my beloved moustache clean off, I look simply horrid" The Doctor knew who was behind this, he also noticed that the most dangerous thing that had happened was the cliff "That's odd, for a being of darkness she's not very…dark, why do I get the impression these obstacles were made by a child" after some complements Rarity had given to the serpent she had enough.

"I simply cannot allow such crime against fabulosity go uncorrected" at that moment Rarity bit off one of the dragons scales and...Cut of her own tail, using her magic to attach it to the serpents face repairing, his moustache.

"Ohh, my moustache! Wonderful!" The Doctor stood in shock he actually liked the way Rarity had her mane and tail done, it was to him incredibly unique and today did not forecast a tail cutting.

"You look smashing" Rarity was pleased with her handy work, but Twilight was feeling sorry due to the loss of Rarity's tail.

"Rarity your beautiful tail" she said mourning the loss of Rarity's tail.

"Don't worry my dear, short tails are in this season, plus it will grow back" she seemed pretty calm despite crying on the inside, The Doctor who was still shock, shook his head and followed.

"Wait a minute! Fabulosity is not a word! Rarity!" running as fast as he could he finally reached his friends sitting by a broken bridge waiting for Rainbow to fix it she later flew back having finished the repairs and the gang having a look on there faces "let me guess ultimatum, them or us kinda thing" The Doctor was still suspicious about the incidents and was putting the pieces together far quicker than even he predicted "take that Sherlock, ha-ha"

"Yea pretty much, but i never leave my friends hanging" Rainbow proudly exclaimed before flying ahead

"At least we're here" The Doctor scanned the room with his sonic screwdriver for Nightmare Moon, just as a precaution while the rest picked up heavy stone orbs and set them in front of Twilight.

"Ok we have 6 where's the 7th" Rainbow asked impatiently.

"The book said that once all six are together, a spark would make the 7th appear, you know this reminds me of that anime I watched last week" The Doctor explained with precision yet complicated causing Apple Jack to interject.

"What the hay does that mean?" she stated unsure of what they were supost to do.

"I don't know, I'm a time travelling Pegasus, do i look like a princesses star pupil, ask Twilight" Twilight herself was not amused with The Doctor s attitude.

"I'm not sure, but i have an idea, stand back" Twilight got into position while the rest were lead out.

"Come on you lot she needs to concentrate" Apple along with everyone else where about to leave then she arrived.

"Girls, heads up!" The Doctor had seen nightmare appear and ran after her as well as Twilight, using her magic Nightmare teleported the elements, The Doctor and Twilight to the tower above.

**In the tower**

"Muhahaha" Nightmare had the elements and Twilight was ready to fight, but a certain Pegasus decided against it

"No Twilight you get out of here, I'll hold her off... and before you say anything remember what i asked you back at the ceremony" looking into his eyes Twilight saw it, the darkness he had inside him, anger, sorrow, regret, he had seen conflict before and he never wanted it to happen again.

"_Trust me...I'm the doctor" _Understanding what he meant Twilight ran off to the side, leaving both Nightmare and The Doctor face to face.

"Stop this, nightmare, it's not too late, think about what you're doing, you could destroy, everything" it was clear that Nightmare Moon was not taking him seriously.

"You're kidding, you're kidding right" she said confident that he was bluffing and just scared of her tremendous power

"I wish I were Nightmare, you may be older by thousands of years, but I'm still pretty old, I know the pain of loss, my entire race is gone!, I don't belong here and I can never go back!, I will never see my friends or family agian!, YOU THINK IM KIDDING! WELL HERES A NEWS FLASH, MISS BAD DREAM, IM A TIME LORD YOU ARE A HORSE, I'VE FOUGHT IN WARS THAT NEARLY DESTROYED UNIVERSES, I HAVE SAVED MORE LIVES THAN ANYONE CAN COUNT" The Doctor had lost his temper and was about to unleash it all in a duel between two forgotten legends "YOU DON'T SCARE ME, and do you want to know why?" The Doctor's outburst affected everyone who heard it, Nightmare especially, it was like she felt his anger and he was telling the truth

"Why?" Nightmare asked with confidence, which lit the spark in his hearts, he was back pony or not

"Because I. AM. THE DOCTOR. And you've been played" his confidence was well placed as Twilight had used his distraction to sneak past her.

"WHAT!" looking behind herself she saw Twilight sparking the elements "_how did I not see her, I didn't feel her magic. It was like another was masking it but he is a Pegasus he can't have magic!" _ Nightmares attempt to stop Twilight would have failed but as if bad luck gave its blessing the elements did...

"Nothing!, that's it" The Doctor and Twilight were gobsmacked, their last hope was destroyed and with an evil cackle and a stomp the stones shattered.

"You little fools, thinking you could beat me! Now you will never see you princess or your sun, the night will last forever!, muhahahahaha" The Doctor was distraught but he knew it wasn't that easy, it never was

"Let me tell you a secret Nightmare, my promise" The Doctors said helping Twilight up from when Nightmare shoved her out of her way.

"What was that a promise to a little filly, pathetic" she asked not knowing of the darkness that lay in his heart, a void blacker than even Nightmares majestic night sky.

"No, to myself, as you may have guessed The Doctor is a title not a name, but to me it is my identity, over 300 years ago I made a promise to never be cruel or cowardly, TO NEVER GIVE UP, NEVER GIVE IN THAT IS MY PROMISE! And as long as my hearts beat and I have friends to back me up i will never break that promise" behind both Twilight and The Doctor were the others, who had heard The Doctor over the lightning which gave Twilight the spark she needed.

"You think, you can destroy the elements of harmony just like that, well you were wrong" Twilight was now as confident as her Ageless friend giving him a final idea.

"that's right, because the power of the elements are right here!" The Doctor now able to hatch the plan he has been cooking since the beginning of the forest, then the pieces of the elements began to lift, causing Nightmare to worry

"What?" she said unsure what was happening?

"Apple Jack, who reassured me during hard times, represents HONESTRY" then three of the shards made their way to Apple Jack and several of the others. "Fluttershy who tamed the manticore with her compassion represents KINDNESS, Pinkie Pie who vanished fear by giggling in the face of danger represents LAUGHTER, Rarity who calmed a gentle serpent by giving something meaningful represents GENEROSITY, Rainbow Dash who would not give up her friend for her own desires represents LOYALTY and The Doctor who helps any and all who need it without a second thought sparking hope to everyone who meets him represents TRUST, the spirit of these six ponies, got us through every challenge you threw at us" nightmare was totally gobsmacked at the fact that each one of her adversaries represented the very elements that imprisoned her

"YOU STILL DON'T HAVE THE 7TH ELEMENT!" Nightmare was on her last legs, trying to get desperate.

"Sorry Nightmare, but we do, I don't know a lot about this world but I know that it is held together by a force even I'm yet to understand MAGIC" The Doctor and Twilight now had the power of the elements of harmony and now intended to use it. To assist the team the elements took new forms for practical use, the five mares elements turned into golden necklaces, with the element housed in taking the shape of the cutie mark of each mare, with The Doctor's turning into a helmet that when worn made him look like a Alicorn (which is what Nightmare Moon is) with the symbol of the galaxy on the side and Twilights took the form of a crown with the element houses as the crown jewel and with the power harnessed the energy passed from the five mares to Twilight to amplify the power then focused and fired through The Doctors new horn, engulfing and defeating Nightmare moon. It was over.

After the battle, all the ponies awoke with a massive headache

"Oww, my head" the first voice to speak being Rainbow Dash.

"Every pony ok?" Apple Jack was the first to check everyone was ok.

"Isn't that my job, i am a doctor you know" The Doctor got up and rubbed his head as all that power was focused through it felt like a hammer to the brain.

"Thought you said it was a promise" Apple was now teasing The Doctor about his little secret.

"It is! but I have a medical degree as well and no I'm not telling you my name!" everyone could see that the relationship between Apple Jack and The Doctor would be interesting to say the least

"Thank goodness!" Rarity was excited to find that her tail had grown back.

"Well at least some pony's happy" was all Rainbow could say to the fashion designer.

"Hey I tell you what I never thought we actually represent the elements of harmony" Apple Jack was now admiring the necklace around her neck.

"that you do" a voice could be heard from out of nowhere followed by a bright light being the sun which had risen once again and in the light stood a majestic Alicorn with a rainbow coloured mane (a lot lighter than rainbows), all of the ponies bowed in respect but Twilight and The Doctor who had no idea who she was, but he got the idea that this was the ruler of Equestria Princess Celestia plus she was not his monarch to bow too, he did not belong here after all.

"Princess Celestia!" Twilight ran to her teacher glad that she was safe.

"Twilight Sparkle, my faithful student, i knew you could do it" Twilight was confused as she didn't not understand the way her mentor had planed the return of Nightmare Moon

"You said it was just an old ponytale" she said remembering the letter she had sent Twilight before she came to Ponyville.

"I told you to go make some friends, I saw the signs and I knew you had the magic inside to defeat her but you could only unleash it once you let true friendship in your heart" while Celestia was speaking with Twilight The Doctor had made his was towards the defeated Nightmare Moon, yet in her place was a young Alicorn the size of a filly she had night blue coat and a sky blue mane.

"Are you ok?" The Doctor asked the young mare who had terrorised millions all because of jealousy.

"Stay away!" the mare was clearly frightened, which proves that she had little control of her actions as the dark mare.

"Hey, I'm not going to hurt you, I just came to help, like i said i would in the first place" coming up behind The Doctor was Celestia for whom it had been so long

"Luna, it had been too long since I've seen you like this, it time to but our differences behind us we were meant to rule together little sister" Celestia revealed the fact the Nightmare Moon was her sister and that her real name was Princess Luna.

"SISTER!" was the reaction from everyone but The Doctor, who stood there looking at his new found friends with a blank look.

"Oh, come on you didn't see this, one controls the day the other the night we are standing in the castle of the royal sisters for goodness sake plus their both Alicorns" The Doctor actually hoof smacked his face this time before turning back to the two reunited sisters.

"Please come back Luna, will you accept my friendship" everyone was hoping she would accept and not explode into Nightmare Moon again, yet The Doctor had one last trick up his sleeve so make her stay as a protector rather than a conqueror.

"I'm so sorry, I've missed you so much big sister" Luna exclaimed with tears of joy flowing down her eyes along with her sister, who was happy to be with her once more after 1000 years.

"I've missed you too" and that is the story of how The Doctor along with the mane 6 reunited the royal sisters. Now take it a away Pinkie.

"This calls for a PARRRRTTTTTTYYYY!" with the day restarted, Ponyville celebrates the defeat of Nightmare Moon and the return of Princess Luna (classic evil imprisoning a relative had to be defeated for release kind of thing, no one made the connection), with Celestia talking to Twilight about living arrangements, The Doctor walked over to princess Luna who was watching the celebration.

"Here, 1000 years on the moon is bound to create a large appetite" The Doctor gave one of the Sandwiches that Twilight made for him to Luna, who took it wondering why this pony was helping her "Why not go over there?" despite her happiness being reunited with her sister Luna, still felt miserable.

"After what I did to them, they would never forgive me" she said dropping her head down in sadness.

"actually you would be surprised, I noticed that you were not in complete control but you knew about the elements, so you influenced Nightmare to setting traps that would test the embodiments of friendship and I'm not one for that kind thing but I do know that they have forgiven you, trust me on that one ok, now eat up" The Doctor did make a lot of sense to the princess and because of that her mood brightened up and she took a big bite out of the sandwich and was surprised at its taste, she had never tasted anything like it.

"Thank you Doctor" she blushed at the weird Pegasus who tried to help her when she wasn't herself and she admired him for it.

"Oh and one more thing" The Doctor said stopping and turning her head to face Luna.

"What is it?" She asked wondering what he had to say.

"the truth of the night, it's not there to be shunned and it never was, it is the night that people take shelter and sleep because they know they are safe to do so, now they can sleep easier knowing they've got you watching over them now, you protect the people when they are most vulnerable, also with a job like Celestia I think she needs some sleep don't you think...good luck Luna" and with that The Doctor walked away from the celebration wondering what he was going to do next.

**Next time on DW: EQUESTRIAN CRHONICLES**

The grand galloping gala, what a stupid name


	3. Episode 2

COURIER: Back again with episode two of Equestrian Chronicles and this is no doubt gonna be my longest story as its supost to follow every episode including the move Equestria girls which I would like to do, but since some episodes are just the odd character trying to do something like the Cutie mark crusader episodes, will not be written in order maybe as a side project after I got though the series that it is in.

P.S. it says in the last episode that the doctor is Brown, he is now grey as the way I tried to draw him looked better grey with a brown mane (ill show later), he is also not THE Doctor but Junior his son just in case you though he was 10th or 11th or something and to finish off he replaced his coat with a bag which hold his screwdriver and other things and he wears a tartan tie around his neck

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Whooves Jr

Ep 02

The grand galloping gala, what a stupid name

It had been a week since the events that took place at the summer sun celebration and the return of Princess Luna; everyone was getting back to their routine but the Doctor who still struggled to adjust to pony life decided to help AppleJ and Twilight with some apple harvesting

"Thank you kindly for helping me out Twilight and Doc, I bet Big Mac that I could get these apples in the barn by lunch time" Apple Jack was in a cheerful mood as she always was with the Doctor and Twilight in tow along with Spike who was picking out different apples looking for one to eat "if I win he's gonna walk down town wearing one of grannies skirts" Apple gave small laugh at the image of her older brother in a skirt

"No problem at all Apple Jack" the Doctor replied looking away from the little dragon throwing away all the apples

"Glad the goal is lunch time, all this hard work is making me hungry" was Twilights response clearly seen with hunger in her eyes

"I know right" Spike commented throwing an apple behind him hitting Twilight on the head which resulted in twilights death glare on Spike

"You've been lounging on my back all morning while we worked" disappointment in twilights voice

"Exactly, you were taking so long I missed snack time" Spike moaned like a child…or a human child

"well you should of said Spike, I would of given you a ruby or something" the doctor had read several books in his free time and packed his newly made bag to meet certain requirements like a gem stash for spike as he learned that dragons eat them as a delicacy "it what I packed my bag for anyway" but before spike could respond he pulled the perfect apple, a bright strawberry red glowing in the sunlight twilight stared at it with lust

"Wow spike that looks delicious" and as quickly as it was shown it was gone "spike!" the doctor shook his head and gave a smirk

"and you just lost a nice apple sized ruby a made for you, too bad" he then trotted past them with a smile as Spike looked in disappointment just before he looked like he was going to barf and like a personal letter box fire burst from spikes mouth and transformed into a letter "well that's handy, whose it from" The Doctor commented as he had never seen Twilight get a letter from spike before

"It a direct line to Celestia, it how we communicate when he are away from each other" twilight explained as spike jumped up to receive the letter. During his first day the Doctor did not see Celestia that often, but when he left after the battle of eternal darkness (as the doctor liked to call it) Celestia came to him for a chat

**Twilight's house, Summer sun-day**

The doctor did not have a key to Twilight's door so he used his screwdriver to open it and proceeded to the west wing, before he could enter the Tardis which was now upright (convenient) and looked better than ever with brand new shade of blue, a tall pony walked came up from behind him

"you are the Doctor I presume" turning his head he saw princess Celestia, her main was definitely her best feature as it flowed perfectly unlike his hair during the time war which would never sit straight, unlike most who would bow he did not as she was not his ruler

"Yea that's me" he answered with a smile which made Celestia giggle

"it seems your reputation precedes you, twilight as spoken all about your bravery to protect her and my subjects from my sister"

"It's my duty to help, I saw many worlds fall in my life and I vowed that none shall ever fall again and this place is no exception" he reassured the princess as he unlocked the door (holding a key with hooves …logic anyone?)

"So I assume we can trust you to defend Equestria when it needs it?" she asked finally causing the doctor to think about his life from the war to this moment, he had to make a choice leave like he always did and find a way back or stay and protect this universe as a guardian of harmony; he turned his head to face the monarch who had a gentle smile on his face one he had not seen since his mother…

"yes, you can trust me princess I will defend Equestria with my life, you can count on it" he said with pride in his hearts and smile on his face _"goodbye father, Izzy, Jacob, we will met again"_

**Present day**

Done with his flash back, looked down to see rainbow dash and Apple jack fighting over…

"spike, what are they fighting over?" without looking the small dragon gave him two golden tickets which read on them "ticket for one, the grand galloping gala?..." raising an eyebrow he gave the tickets back "what I weird name, fits but still weird, so let me guess twilight got one and spare and now Dash and Apple are fighting over the ticket" he asked which spike followed with a nod

"we'll look at that I don't know about you but I can't think on an empty stomach, so I'll think about it over lunch and I'll get back to you two ok" as twilight walked away the doctor followed felling peckish himself with Spike on his back while behind them Apple and Dash began a hoof wrestle

Later on in ponyville the doctor and twilight with their sidekick spike walked though town looking for a place to eat

"so who are you going to give the ticket to Twilight" the doctor said with a worried look, he knew that the one thing harder than a life or death choice is a choice of which of your friends go somewhere with you

"I don't know doctor but I really can't think straight when I'm hungry, so where should we eat" and at the most unlikely of times a pink blue bursts out a door and into the trio, after the tumble the two tickets floated in the air lightly landing of the nose of the infamous pink party pony

"Ahhhh something on my face heeellllp, wait! These aren't" stopping for a minute to confirm her eyes the only part of her body that wasn't pink "THE GRAND GALLOPING GALA!" then she started singing followed by the doctors ears turning off "Ohh thank you twilight it's the most wonderful gift ever" both purple and grey ponies stared at the ecstatic pinkie as she though the ticket was for her

"well at least rarity hasn't seen them yet" the doctor said at the wrong time as he picked up the tickets only to find the heavenly white unicorn standing in front of him

"Are these what I think they are" she said with disbelieve

"Bollocks" was all the Pegasus could say taking a few steps back from the clearly dangerous, generous beauty in his presence

"Yes, yes, yes, twilight is taking me to the grand galloping gala in canterlot" was pinkies answer to rarity's question followed by a sparkle in the white unicorns eyes, mane too

"the gala…I design ensembles for the gala every year but I've never had the opportunity to attend, oh the society, the culture, the glamour, it where I truly belong" she said with the posh accent at its maximum

"Of course you do" the doctor hoof palmed himself with his sarcastic comment

"And where I'm destined to meet…HIM!" again followed by a hoof palm

"of course you are…again humans, ponies are mentally no different" he said before walking off as rarity explains her supposed fool proof plan at a royal wedding "you know in my universe every little girl has the same dream and like you they will fail, in fact if any one of you becomes related to a royal family i will pay you 100...gold coin things you use" not realising he had made a terrible mistake for the days to come

"still I cannot believe you would invite pinkie so she could "party"" saying it like it was frowned upon "and prevent me from meeting my true love, how could you" she said finally turning away with her nose up and like the world was trying to give the doctor a double heart attack a small white rabbit shot up and nicked one of the tickets and ran to give it to flutter shy

"The thing is I haven't decided who will get the extra ticket" as soon as twilight mentioned this, both pinkie in disappointment and rarity in excitement, responded how anyone would really act

"YOU HAVEN'T!" both ponies exclaimed accordingly, than a very quite yet gentle voice spoke up

"Uh, excuse me…twilight, I would just like to ask if it would be alright, if you haven't given it to someone else" but rarity was surprised as Fluttershy was godly shy and she assumed she couldn't have a reason

"You!, you want to go to the gala" she said raising an eyebrow which then Fluttershy when on to explain her reason for wanting the ticket, however the doctor had enough and decided to head to what looked like a burger place, about a couple of days after his arrival Celestia had kindly given him a small allowance to buy certain things like clothes and equipment, so he kept his wallet on him in case he needed something. After entering the restaurant which was called the hay shack, the doctor examined the menu, it appeared that all the food ponies eat was considered healthy for horses on earth but the hay shack clearly resembled a fast food joint then a bright green mare with orange hair (yes not ginger, orange) looked at the grey Pegasus with a smile from behind the cash register

"Hello, sir may I take your order" catching the doctors attention he made his way over and made his choice

"Yea, sorry can I have a big hay with…is that cheese?" he asked not knowing if ponies collected milk

"Yes sir, that is a big hay with cheese and anything else?" she asked resulting in the doctor checking the drinks

"If you don't mind me asking what is in apple cider?" the young mare raised an eyebrow as the stallion acted as if he was just learning what was in the food that he ate

"It is one of the apple family's tuned down recipes, so it isn't as strong as the home made one" after a brief explanation the doctor was finally satisfied

"Then I'll have a large one of those as well, seems I'm a lot more thirsty than hungry" this seemed to be his signature trait as the cashier gave a small giggle at the doctors charm

"of course sir it won't be a minute" after his food had arrived he decided to walk back to the library and eat there, about have way there he stopped in his tracks to see twilight running past with what looked like the entire female population of ponyville, seeing the cashier that served him in the mob

"Well seems the entire town knows now, poor Twilight" after they passed the doctor crossed the path only for another group follow up behind them and trample over him leaving him near cripple on the floor with his precious lunch only an inch away "must reach food!" he said with pain in his voice only for a small filly run past stepping in the bag crushing the food and spilling the cider, the little one stopped realising she had stepped in something and her reaction proved she was sweetie belle, rarity's little sister

"Eww, I stepped in someone's lunch" looking back to see a horrified Grey Pegasus as his eyes where completely dead "oops, sorry mister" getting up from the ground looking at his destroyed salvation he stood on his hind legs only to collapse on them again

"NOOOOOOOOOOOOOOO!"

_**Later on at twilights house**_

After returning to the library the doctor collapsed on the couch being the time lord equivalent for starving, diced t sleep and get some dinner when twilight come back, he began to close his eyes when I bright flash blinded him for a brief second, upon his returning vision he saw twilight and a scorched spike, rushing to close all windows and dim the lights

"Twilight, that won't work because…" before he could explain the lights turned back on and their friends were right behind them

"Oh for Celestia's sake, I can't decide as your all my friends and I can't let one go without the others being angry or sad" twilight was on the verge of a mental break down and all six of her friends could see that that was when some stepped forward

"Twilight sugar, I didn't mean to put so much pressure on you and if it helps I don't what the ticket no more, you can give it to some pony else, I won't feel bad, I promise" apples little speech drove the rest to tell her that they didn't want the ticket ether apart from rainbow at first

"We're sorry, twilight" the five girls spoke in unison however there was a very irritated and hungry time lord also in the room

"Well it's your greed that cost me my lunch, well actually it was rarity's sister but that is cruel blaming a child so I blame all of you, you own me a big hay" after the apology and the doctors little out burst she stood up and signalled spike

"spike take a note, dear princess Celestia, I've learned that joys of friendship is sharing your blessings but when there is not enough blessings to go around having more than your friends can make you pretty awful, so I appreciate the invitation, I will be returning both tickets to the grand galloping gala" this caused every one doctor excluded to gasp in shock

"WHAT!" they all shouted in unison

"I my friends can't all go, I don't want to go ether" the doctor had seen that twilight was a pony of her word, but he had something crawling in the back of his mind

"hey I've just realised, if the princess is your teacher and you know her pretty well won't she be able to just give you extra tickets" he said as spike sent the letter making everyone else think

"ya know what I think your right doc" Apple replied as spike began to barf, blowing out green spoke which turned into a letter and almost taking apples head off "whoa Nelly"

"well speak of the devil" as the letter landed all the girls turned, unsure of his comment "it's a saying, you know when you're talking about someone and then they show up or they are mentioned…never mind" all they girls laughed as the doctor just gave up in his attempts, and opened the letter "my dearest student twilight why didn't you just say so in the first place, SEE!, I told you, you could of just asked anyway here are 7 tickets to the gala" all the girls gasped causing the doctor to hoof palm himself

"You really need to stop doing that" spike said to his grey friend

"Can't help it, these girls are just bloody thick sometimes" he said before handing out a ticket to everyone leaving one in his hand

"allow us to treat you to dinner" rarity told twilight as they all left with their tickets apart from spike who began walking up stairs

"Spike" the little purple dragon who felt left out as he didn't get a ticket turned to face the doctor "here take it"

"Huh?" spike said confused as twilight had a reason to not go but the doctor didn't

"I don't want it, and I think Celestia knew that so this one is yours" taking the ticket, spike ran out the library with a childish laugh passing apple and instantly dismissing his desire to go, with spike barfing up yet another letter with a tag on it

"Hey doc, it's for you" the little dragon gave the Pegasus the letter before running off, curious he opened it, it read

_Dear Doctor_

_ I understand your desire not to go to the gala but would you please as I will be busy with the guests and Luna will be alone the entire night all I ask is that you give her some company_

_Yours sincerely Celestia_

_P.S. I would suspect Luna would appreciate it if you turn up, she seems to have taken a liking towards your kindness when you first met_

In the letter was another ticket which the doctor placed in his bag and walked off towards his friends, to continue his search for food

"_Seems I'm going to need a suit, RARITY! I NEED A FAVOUR"_

**Next time on Equestrian Chronicles**

**THE SONIC-TIME BOOM**

_COURIER: Thank for the support, everyone and I would like to take a mo explaining the episode order as next takes place after the sonic rainboom episode and is like half a series way._

_DOCTOR: Yea why is that anyway?_

_COURIER: I'll tell you, you see the every season takes about 23-26 episodes, apart from season 3 which was 13 and a movie, but so I have time for more original adventures I'm only doing episodes that are connected to the final two-part finally or if they are really good and maybe if people vote for one. So I have to admit Ididn't like this episode but it is connected to the key point of this story which is a bond between both the Doctor and Luna._

_DOCTOR: Wait, what? Me and Luna._

_COURIER: She didn't get enough screen time and I like the similarities between The BBC Doctor and My Doctor as both live in their shadows and have dark legends of their own._

_DOCTOR: Oh, ok cool, any way if you have any questions for me or Courier, just visit the brand new tumbler page at _

_COURIER: Need to use it for something, however I have limited knowledge of tumble so, if you don't have tumbler just pm me but I would prefer on tumbler…OH and one more thing this chapter in the Chronicles Saga is the one most people like (which makes me happy) so the more people read the faster I make stories and give me some ideas for episodes if you want I just won't tell which ones I'll use thanks again. Bye guys._

_DOCTOR: See you._


	4. Episode 3

_COURIER:_ Hey guys this is a story I've had under my hoof for some time, it's just to show that the doctor isn't just brains when in I dire situation. It also builds up the development of the bond which is forming between Luna and The Doctor. Well enjoy

Disclaimer: I do not own MLP: FIP OR Doctor Who and I'm only doing this because I want to

Doctor Who:

Equestrian Chronicles EP 03

**Sonic time-boom**

It has been a couple months since The Doctor had landed in ponyville and helped the mane six defeat Nightmare Moon; it had been a very interesting day for him as a contest for best flyer was being held in Cloudsdale and since he was a Pegasus he decided to go and cheer for Rainbow Dash (considering that the only other Pegasus was Fluttershy, he thought it was the smart thing) but later on everyone could come, yet Rarity had grown some butterfly wings (courtesy of Twilight) which in the process made Rainbow more nervous than she was. During the contest, which the first prize was a day with the Wonderbolts, Rarity entered at the last second and ended up showing of her wing which had dissolved in the sun causing the Wonderbolts to intervene but ultimately Rainbow had forgotten about the contest to save her friend.

"Hold on Rarity!" as everyone marvelled at her speed, The Doctor knew what would happen (he knew nothing of the sonic rain boom outcome).

"Doctor are you ok?" Twilight asked The Doctor who had his head almost below the balcony, hoping he wasn't going to be sick.

"Twilight! You don't understand! At the rate of her velocity and her wings giving the right momentum!" The Doctor shouted in Twilights face with glimmer and joy "she could break the sound barrier, producing a SONIC BOOOOOM!" and as he finished Rainbow had indeed broken the sound barrier and the colour of her mane was all that remained as the sonic boom and the trail behind her was a perfect rainbow. Now knowing he could potentially break the sound barrier, The Doctor had an idea.

**A WEEK LATER**

Sitting on a cloud The Doctor was applying bandages to his head and legs while he was doing so didn't notice Rainbow Dash creeping up behind him.

"Uhh, Doc what are you doing?" The Doctor turned to face the rainbow coloured Pegasus.

"Well, Rainbow I am a scientist and watching you break the sound barrier was something I never considered, so I am attempting to do the same, but I did fail a couple of times" he explained showing Rainbow all his bruises.

"Well, I am pretty awesome, but I don't think you can do a Sonic Rainboom, no offence?" the stallion of time gave a quick smirk.

"None taken, and I'm trying to create a normal sonic boom, the rainboom is unique to you and you alone. You see when anything breaks the sound barrier, they become too fast to see clearly so their colours follow them, since your mane is Rainbow coloured you produce a sonic rainboom" enlightened by her small lesson Rainbow Dash forgot what she came for.

"Oh yea I forgot, Twilight told me to get this too you urgently" she handed him a letter stamped with the royal seal also giving him a salute.

"My faithful student Blah, blah, blah, I require you and your friend to come to Canterlot urgently" after reading the letter he stuffed it in his bag and both time and rainbow ponies raced to the capital of Equestria, it was obvious that The Doctor was now used to his wings and had grown to flying so well that he could almost keep up with rainbow at full speed.

**OUTSIKRTS OF CANTERLOT**

Once within eye sight of canterlot, it became apparent that something bad was happening as the castle was damaged and buildings were burning and collapsing.

"What happened here?" Rainbow was shocked, at the revelation before her eyes.

"I don't know, Rainbow go ahead and help out, I need to see Celestia" with Rainbow breaking off the doctor landed in the castle via the big hole into the throne room, inside he saw princess Celestia comforting Luna, who looked gravely sick with her night blue coat's colour fading in and out "Celestia!, what is going on?" Celestia's face was full of concern, knowing that she was faced with an ultimatum.

"Doctor, it's Luna, she is terribly ill and can't control her magic which is causing destructive waves of energy, but I can't leave as the first time it caused most of the damage you see now" The Doctor knew her situation and was thinking of a way to fix it, mainly for Luna as she was the source to helping her would allow time to recover and repair the damage.

"Ok, let me have a look at her, I've read enough on pony anatomy to be an actual doctor for ponies" taking off his bag he pulled out several medical tools, Luna tried to speak, but she was too weak to even move and struggled to say anything.

"Doctor?" she asked recognising his voice. He then began examining Luna.

"Don't speak Luna, save your strength, don't worry you're going to be fine" The Doctor reassured Luna and she closed her eyes resting, with a small smile on her face. Celestia however was worried about her sister, afraid that the city would shun her since she was the most feared pony in history, reformed of course, that had almost destroyed part of canterlot.

"Will she be alright?" The Doctor took out a thermometer from Luna's mouth, it surprised her that Luna was actually letting The Doctor help her _"she wouldn't even let the royal physician come near her yet she allowed him to help her, he didn't even have a medical degree…so that's why he represents the element of trust"_

"She's not good, it looks like she's fighting an infection" The Doctor could of helped her if the damage was physical, but he knew nothing about illnesses to ponies "Celestia, did you have her examined after she returned?" Celestia knew this sort of thing would happen.

"No, I tried, but she wouldn't let anypony near her when it came to medicine, in fact you're the only doctor to examine her. The Doctor placed his hoof on his chin and began to think, and then it hit him.

"Hold it, Princess I'm guessing that, the medical technology of today wasn't present 1000 years ago"

"You are correct" she confirmed realising were he was going with this "know that you say, she hasn't aged, since her banishment"

"So, which means that she is ill with a disease, that was present a millennia ago, that would have not had time to take affect" the princess now knew what had made her dear sister ill.

"No! The Discord fever! How could I be so blind?" The Doctor had no idea what she was on about, but by the sound of her voice, he knew it wasn't good.

"Why do I get the feeling this was mistaken by disco fever" ignoring his comment the princess used her magic to bring a book, which was very old but well maintained, opening the book to a page near the back.

"It was an illness made, by a wicked being known as Discord, he was the embodiment of disharmony and chaos and had the ability to control the fabric of reality, after his defeat an illness soon appeared Around the Equestria, which caused spontaneous magical outbursts in unicorns"

"And since alicorns are part unicorn they are affected as well" The Doctor now had the jist of it yet he just needed a cure.

"Correct, it is recoverable so this is only temporary, but the magical outbursts will destroy canterlot before she can recover" The Doctor needed a place where she could heal without causing too much damage.

"I know a place where she can heal but it can't get here, so I need to carry her" the princess shook her head in disagreement.

"You wouldn't make it, the outburst at full power are too much for anypony, you would not survive, I can barely, keep the blasts suppressed. But I have something that could help" using the same technique she brought the book with, she had now brought a bottle of green liquid "this will dull the effects of the fever but It lengthens the time of recovery" The Doctor took the vial then gave it to Luna.

"Luna?" The Doctor tried to get the attention of the weak princess, not opening her eyes or speaking but stirring as a response "please drink this, it will dull the illness so I can treat you better" hearing his voice, told Luna that she was safe proving so as she slowly opened her mouth and drank the contents of the Vail, followed by a nasty cough "that bad huh?" the taste gone from her mouth she returned to her slumber with a gentle smile on her face at his humorous comment while also regaining some of her colour "Celestia" The Doctor asked in his serious dark tone that he had used against Luna as Nightmare moon during their battle while getting up from Luna's side.

"Yes?" the princess, heard about this pony from her student, about his dark atmosphere that she heard even her sister was scared of, and she could see why.

"I need, my element of harmony, with it I have the full abilities of an Alicorn so I can teleport her" following his instruction she left to open a vault which only she could open and she returned with the element of trust.

"Here is the element, please bring her home safe" The Doctor packed his bag and placed the element on his head, making him look like an alicorns with the helmet on.

"I promise, she will be fine…tell the others I'll be back" harnessing the powers of the element The Doctor attempted a spell that Twilight had shown him, a transportation spell, focusing on the library he noticed something else, it was everywhere, the same thing everywhere at once and only one thing was like that "Avanti!" and in an instant both Luna and The Doctor vanished and Celestia left to assist her subjects.

**At the tardis**

In a flash of light, both the ill princess and the time traveller, where now in a large room with a six panelled console in the middle of a platform which was raised above the floor The Doctor stood on.

"I knew it, only the tardis could be everywhere at once, now to the zero room" his little excitement over, he used his magic to lift the princess on his back and moved in the direction of the zero room. The zero room was a very special room meant for meditation and healing, just being here would heal most injuries in half the time, but infection would be healed in even less "here we are, been a long while since I visited here" The Doctor had set up a bed in this room since he liked to sleep in here every now and again, it was incredibly beautiful as it was modelled to look like a garden on Gallifrey. Now placing Luna on the bed, he took off his helmet and placed it on a table, which Luna would recognise when she woke up, exiting the zero room he turned a dial near the door which moved the sun in the zero room over the horizon bringing out the moon and The Doctor noted that Luna's mane had become more majestic in the moon light, he had never actually seen Luna at night "sleep well Luna". Now making his way out of his ship and out Twilights library he spread his wing ready to make a return trip to canterlot, his bandages also fell off as being in the zero room healed them quicker than even he could naturally do. Taking off, he raced towards the capital to assist in any way and he flew, in fact he flew so fast he made it in half the time.

**AT CANTERLOT**

The mane six and Celestia with many others were helping free the ponies from collapsed buildings and rushed them to hospital, but in the process rainbow burnt her wing while saving several people from a burning building, but she then noticed something flying very fast in the distance.

"Wait, who is that?" curious to who could fly that fast, a crash could be heard and turning round, she saw the castle tower had lost it integrity and had broken off. Closing in was The Doctor hell-bent on saving lives and below the falling tower was the hospital, knowing that there was no time, he lowered his altitude and aimed for the hospital, his friends saw their friend race to his target and just has he reached the wall…it happened, he had flown so fast he had reached and surpassed the sound barrier, but instead of the Sonic Rainboom even a regular sonic boom, there was nothing his body became engulfed, in electric energy that when he passes the wall …there was nothing, no Doctor, but on the ground was a trail of flames along the straight road, everyone stared at the trail left behind by the time travelling pony, and looked to the imminent fate of the patients at the hospital. However by The Doctor's view everything had slowed down, he saw the flames on buildings burning slow, the noise deeper and longer _"I did it I broke the sound barrier, but not in the way I pictured it" _taking advantage to his new ability, he flew past homes, the market and several ponies on the street all while leaving a strong gust of wind behind him in real time to everyone else. Reaching the hospital he flew in the window and grabbed as many as he could and moved them to a safe area, taking all the time he could, he made several return trips finally, only several children remained, grabbing them and flew to place them with the nurses who had moved to find themselves in the garden but still moved to slow by the doctors point of view, now the rescue op complete he flew to his friends using his wing as air breaks to slowdown, upon a sudden drop in speed, his hooves caught the ground, and made the same flaming trail he had started with. All his friends including Celestia were shocked to find that he had just saved thousands of lives in less than couple of seconds, even rainbow could not believe it but in the same second she saw the burning trail the first time, the large population of the hospital was in the garden.

"How did you do that?" was The Doctor's best friend Twilights question that everyone wanted to hear.

"I broke the sound barrier, you see ever since I arrived in this world, I have been practicing flying, and since I had no idea how to, I based my movements off Rainbow and in about a month I had learned how to fly and every week I timed myself going round and round, ponyville, my time getting quicker and quicker, the reason I didn't get here sooner in the first place was because I was injured and I wouldn't leave Rainbow behind, so when I dropped off Luna, I unleashed my full speed and made it here, but when I was trying to break the sound barrier, I crashed and hurt myself several times, but I was so focused on helping people, when I saw the falling tower it just clicked and next thing I know is that I'm flying at normal speed and everything was moving at a thousandth of a second, so I rescued everyone in several minutes by my point of view but by yours I was literally a split second, cool huh?" he explained looking like a very happy puppy, near the end of his explanation. looking back he saw the flaming trail he made "oh my God, that's what happens when I travel the sound barrier, oh that is just smashing, I'm like a de'loren on hooves" everyone was shocked that he was actually faster than Rainbow, she herself was trying to calculate it in her head, she was flying at her full speed without trying to use the sonic rainboom, surprised that the doctor could keep up, but he was faster all along and it was only his injury's that slowed him down.

"Hold up! How can you be faster than me?" Rainbow stated with anger and annoyance with The Doctor and as usual he was lost and confused at her question "well speak up" now with her face in The Doc's it was now more difficult to explain himself.

"_Bugger, what do I do now" _thinking off a strategy that could get Rainbow of his back "it's because I am more mature"

"What is that supost to mean?" she began to raise her voice even more.

"It means that I can roughly travel at the same speed may be slightly faster than you because I'm older and my wing's are more developed! In my world people don't usually fly naturally so machines were made to allow flight, in the development were scientific ways to gain altitude and momentum and since you ponies never needed artificial flight you never thought of different flight techniques! It's the reason I lost altitude before passing the wall as gravity would of allowed me to fly faster but I didn't could on breaking the sound barrier!" The Doctor now talking serious as to force Rainbow to back down "don't you see, you are an incredible flyer and will have more experience than I will for quite some time, but my own experiences and ability to think outside the box in terms like this will allow me to surpass you, plus your only 16, I'm over 400 and my body is technically still a Time Lord so my body is developed accordingly probably which is why my wings are more like an alicorns than a Pegasus. So I'm sorry Rainbow but the fact I'm faster can't be helped" rainbow now saddened by his explanation walked off with her head down.

"Yea I guess your right" as the other five of their friends along with Celestia stood watching The Doctor deal with Rainbow, the time lord walked over to her and past her without looking at her.

"But remember this Rainbow Dash, no matter how fast I fly or if I beat you in a race I will never be the fastest pony in Equestria" Rainbow regained some integrity and wondered what her strange friend meant "it because I don't want to be, I was the best on my world, I could match anyone in math, science, engineering, I could of become the most famous Time Lord of my time but I decided to become a teacher and my life was defined by war and then loss followed by the drive to explore and discover. Why I'm here I have no clue but why you're here is crystal clear, you have the power to define yourself though your talents like every pony else, but my talent is not fixed, now I've explained myself, Rainbow are you going to let that stop you from becoming the greatest" looking up from the ground an into the Ancient eyes of her friend from another world she raised and shook her head.

"No I will be the best, sorry for getting mad at you Doc" putting a smile on his face, one question that only the doctor could answer was in the princess's mind.

"Doctor, my sister is she safe?" The Doctor turned to his friends mentor to give her some good news.

"She is fine as soon as the potion we gave her wares off my Ship will keep her energy contained and protect her from harm" the mane six were still puzzled to the cause of the developments that they still had questions.

"Doctor, what was wrong with Princess Luna?" Twilight ask as he finished reassuring Celestia.

"Luna was the victim to a virus, that affects unicorn magic and being an alicorn is no exception as it seems to affect magic directly, she is right now in my Ship recovering with the help of some of my native technology" now informed the 6 headed to the damaged palace in order to discuss the repairs of Canterlot, The Doctor was about to follow but not before clearing some facts to the crowed that had followed the flaming trail he had left behind "Citizens of Canterlot!, this event was an accident and no one is to blame, now that the crisis is over I ask you to assist in the recovery of the city and to never speak of this day again and to show I am serious" the doctor brought out his sonic screwdriver making the public wonder what the device was, after activating it every camera in the area was destroyed along with any pictures concerning the day that had past "your cameras are destroyed to prevent photographic evidence and if I find one article even one sentence of what happened here I will make sure you lose everything and trust me when I say I have the power to do so!" now walking away from the crowd which was shocked at how this one pony could address the public with such a calm and frightening voice and demand their silence.

"Thank you for protecting Luna" Celestia gave The Doctor her gratitude as if Luna found out she had done this it would leave her heart broken.

"She doesn't deserve to live her second chance in the fear of being feared by others" the doctor walked to the wall surrounding the city and spread his wing ready for the flight back "I'm going to check on Luna, I'll be back" showing his incredible speed he shot off in the direction of ponyville and in mere minutes landed (rather badly) in front of Twilights house, leaving a descent sized crater at the door "oww, that hurt, it seems I need to work on that landing" now racing into the TARDIS he entered the zero room to see Luna sleeping peacefully now with her colour fully returned "thanks old girl for taking care of her" the TARDIS discreet humming changed tone as a response to it lifelong owner and friend.

Returning from canterlot the mane 6 returned to their homes and ready to go back to daily life's, however The Doctor never came back with Luna causing Celestia to worry more and more asking twilight to check on her upon her return and she was definitely surprised to say the least, before opening her front door Twilight could hear laughter opening the door she saw on the couch the Princess and The Doctor laughing their faces off and in the chaos The Doctor noticed his purple friend at the door (after falling off the couch of course).

"Twilight I was just telling Luna about the time that I crashed onto a snow covered planet and in the process angered a Hugh Bear like beast and ran away nearly wetting myself in the process" continuing with the laughter Twilight giggled a little herself happy that the princess was well again.

"Well I just came to say that Celestia is still a bit worried it would make sense to release her of the stress" getting up from the couch Luna walked over to twilight and to the door with a happy smile on her face.

"Yea I suppose you're right, I mean I would also be worried if Celestia was hit by the debris instead of me. It just sad that I could not help any pony else during the earthquake" Twilight was confused there was no earthquake, was it possible she is suffering from amnesia from the affects of the virus "thank you again Doctor you have been a great help" giving off a small wave and a smile The Doctor said his goodbyes and Luna disappeared using her magic.

"Doctor, does she not remember" The Doctor still with a small smile shook his head as an answer to his friends question.

"No, before she woke up I wiped all memory of the incident from her mind and explained when she woke up that an earthquake had struck causing the structure of the Castle to break apart and she was hit by debris after helping save a couple of ponies, I also sent a letter just a few minutes ago to Celestia to never speak of it again, she should be done explaining it to her subjects now" Twilight's relive was turned to anger as The Doctor had messed with someone's memories without permission and (as she though) experience in doing so .

"Doctor that was reckless!" now confused The Doctor got up himself not knowing what Twilight was on about.

"What was?" he said cocking his head a bit.

"You can't just use the elements of harmony play with someone's memories like that and you may be able to fly perfectly now but you still know little about magic especially alicorn, you could of seriously damaged her mind" Twilight had believed that The Doctor had used the element of harmony that gave him the power of an alicorn to alter Luna's memory but she was the one at fault and The Doctor's atmosphere was dulled once again like it did when Rainbow confronted him about his ability to fly.

"Yes, your right I don't know much about alicorns but I didn't use the Element" Twilight and The Doctor were prone to argue but over little things, this was a battle that had never been considered.

"What do you mean by that?" Twilight asked wanting to see what kind of explanation her lodger could give.

"This isn't the first time I've altered someone's memory and I didn't use the element because I didn't use magic and I know a lot more about the mind than you do Twilight's if you want to continue arguing about the method then listen to the reason!, she lived for 1000 years alone and upon her return she was feared and when we stopped her dark side and brought Luna back she was still afraid and alone, imagine if she knew she was the cause even unintentionally of the events that have occurred today" Twilight now could see where he was going and felt sorry for doubting her best friend.

"I…I, She" as she too like Rainbow was beginning to tear up over her misjudgement The Doctor walked over and hugged the Purple unicorn.

"She would feel even more detached and lonely, we are her only friends and even still we don't see her that often, did you see her face when you walked thought that door, that was probably the first time she laughed that hard for a millennia and I forgive you Twi for questioning my actions as you were also concerned for her health, but let's just be glad that she is now happy that she has friends that she can rely on ok" now braking off from the hug The doctor dried off some of Twilight's tears and Spike walked in not knowing what was going on.

"Hey guys, what I miss"

_**Next time on DW: Equestrian Chronicles**_

Trixie: I am the great and powerful Trixie and anything you can do I can do 3 times better

Doctor: bet you can't go back in time and say hello to your self

Future Doctor: Yea, that I'll be the day

Apple Jack: Sweet Celestia there's two of them

GREAT AND POWERFUL TRIXIE VS THE LAST SON OF GALLIFREY

**COURIER**: I found this chapter very good, please review and give me any feedback on what could be improved or about your thoughts on episode 4. Any way thanks and have fun you guys


	5. Episode 4

COURIER: episode four, the battle that will shape the very fabric of time and space…

This episode will not include the big bear but instead a duel of tricks and wits, HAPPY PONY GAMES AND MAY HARMONY BE EVER IN YOU FAVOR…ooh that's a really good idea

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Who:

Equestrian Chronicles

**Ep 04**

_THE DOCTOR VS THE GREAT AND POWERFUL TRIXIE!_

"Come on Twi" The Doctor along with spike were urging on Twilight as she practiced her magic, The Doctor usually works on the TARDIS but some of Twilights tricks sparked his interest and volunteered as attest subject along with spike

"You can do it" the little dragon also urging his owner and friend

"Ok here goes" as Twilight reassured herself she charged up her magic and unleashed it on the Time Pegasus and dragon causing moustaches on both of them

"Ha ha you did it!" spike congratulated twilight on a successful test while The Doctor was…

_(LIGHING AND THUNDER AND EVIL MASTERMIND MUSIC IN THE BACK GROUND)_

"MU HAHA, I the great and powerful Doctor Rassilon will rule all of Equestria as the pony Lord of Time" Spike and Twilight wondered how the music and lights happened and both thought he was planning this from the beginning

"Sorry Doctor, it's just for practice and it's got to go" Twilight deactivated the spell causing the Doctor's moustache to disappear as well as the effects puzzling both of The Doctors roommates again

"Aww, I looked epic, in fact it reminded me of my godfathers moustache when I met him, dam he was a lot of trouble, I think he's reformed and scarified himself at the end of my dad's 10th self, he never explained the details"

**IN THE TOWN CENTER**

Both The Doctor and Twilight were strolling in the Equestrian sun, discussing different topic they've been working on

"Still 25 tricks and counting, you're developing quite the arsenal" The Doctor was writing in his note book (using a device that held his notepad and embarrassingly asked the ponyville school teacher to help him write with his mouth)

"You think, I think its great practice" Tw ght said with her usual smile. As the two ponies enjoyed ili the day and continued walking two more slightly younger ponies ran past and somehow dragging the doctor with them

"Ahh, he let go" The Doctor screamed trying to use his wing but before he could they stopped causing The Doctor to go flying and crashing into the side of a house "logic! You traitor" he stated as he got up and dusted himself of "all right! You two start talking"

The two known as snips and snails (why someone would call their son snails I have no idea) both looked extremely happy and where heading for the town square "haven't you heard, there is a new unicorn in town!" snails explained like it was common knowledge

"yea, they say she's got more magical powers than any other unicorn ever" snips also explained while jumping up and down

"Well unless her special talent is magic with a side dish of ketchup, I don't think she could match up to someone like Twilight or me for that matter" he said in a calm and controlled voice unlike the other two

"Well you'll have to see for yourself come on" snail explained and both raced to the square with both The Doctor and Twilight in tow

**TOWN SQUARE**

Nearly the whole town was gathered in the town square to witness the power of the unicorn known as Trixie

"COME ONE, COME ALL WITNESS THE INCREDIBLE MAGIC OF THE GREAT AND POWERFUL TRIXIE" she announced her self well rolling the R in her name and the little shack in front of the crowd had opened up in to a stage and she appeared out of smoke "watch in awe as the great and powerful Trixie performs the most spectacular feats of magic ever witnessed by pony eyes" this time exaggerating her words with fire works

"my, my, my, what boasting" the fine example of Rarity gives her comments as she details that Trixie is showing off, with spike also sharing her opinion

"come on, no pony is as magical as Twilighiiii" spike instantly realising who he was standing next too, The Doctor had discovered on his second day as a pony that spike had a massive crush on rarity which he thought was weird since they are both different spices but he could recall from experience if you live with a species long enough you can the attraction "hey Rarity…moustache!" he exclaimed before dashing off confusing Rarity in the process

"Nothing's wrong with being talented is there" Twilight asked since she was clearly talented and was worrying about her friends reactions to Trixie

"Nothing at all, except when someone goes around showing it off like a school filly with fancy new ribbons

"I'm going to pretend I understood that Apple" The Doctor said since he was oblivious to most of the metaphors AppleJ used

"well that's your problem, mister smarty hooves" Apple responded with her strong Texan accent

"Just because that one has the ability to perform lots of magic does not make one better than everyone else" Rarity explains and pretty well

"Especially if you got me around being better than everyone else" Rainbows statement bought a death glare from both Time lord and farmer "I mean magic's shmagic boo" she tried to correct herself as not to face the wrath of the two together, however this discussion caught the attention of Trixie who was one to protect her reputation

"it seems we have some NEIGH-say'ers in the audience" the instance that she did that The Doctor heard uncontrollable laughter in the back of the crowd, he too found Trixie's cliché horse sound hilarious but unlike the brown stallion at the back he controlled his amusement "who is so ignorant as to challenge the magical ability of the great and powerful Trixie, do they not know that they are in the presence of the most powerful unicorn of all of Equestria"

"Pfff, cheap parlour tricks combined with real magic, that's nothing special" The Doctor could take from experience he had met some of the most famous magicians in his universe "she's a 2nd grade magician at most" however Rainbow never backed down from a challenge

"So great and powerful Trixie what makes you think you're so awesome anyway" rainbow using her 'not loud at all' sort of touch

"Only the great and powerful Trixie has the power to fend off the great URSA MAJOR"

"I would like her reaction to a weeping angle, the cocky witch" The Doctor was known for insulting people for little reason but Twilight had no idea what a weeping angle was and knowing the doctors experience didn't want to know

"it is true Trixie is most certainly the best in ponyville" it seemed that Trixie would continue boasting and wanted to show off her talent "don't believe the great and powerful Trixie" she said in on second long shot "well then herby challenge you ponies of ponyville anything you can do I can do better" the thought rushed through every one of the mane 6's head to put her in her place and of course one was bound to stand up "or is Trixie destined to be the greatest equine who has every lived" Spike who had his mouth zipped for some reason was begging twilight to outshine her but that was before Trixie challenged Twilight herself but after a bit of hesitation it turns out she was talking to Apple jack

"That's it I can stand no more of this" she announced walking up the stage and she began to show a little of her talent "can you little magic do this" and of course she was amazing as she was doing robe skipping near perfectly with the rope bound to her tail and than using the rope to pick an apple which landed perfectly in her mouth "top that missy" and of course Trixie had a trick up her hat

"oh ye of little talent watch and be amazed at the magic of Trixie" and taking off her hat to use her horn she possessed the rope like a snake which actually mesmerised AppleJ and went off to pick an apple before tripping and binding her legs together and stuffing the apple in her mouth like a pork amazing the crowd after rainbow also tried and failed to win and the embarrassment of Rarity, this was the last straw

"Ok that's it this has gone on long enough" The Doctor stood up onto the stage and was ready to put Trixie in his place

"And what can you do that the great and powerful Trixie can't" she said with confidence unknown of the Pegasus which she enraged

"Bet you can't go back in time and say hello to yourself" not many ponies knew The Doctor but he was good at what he did second to none

"That would be the day" and like that another pony walked from behind the curtain wearing the same Tartan tie and same colour mane and coat, in fact looking closely it was the same pony, there were two doctors

"Sweet Celestia there's two of them" Apple jack said in shock, both Doctors stood like one looking in a mirror and both looking at Trixie who was shocked to say the least

"So what, using you twin isn't magic" the suppose future Doctor smiled while looking at the present doctor

"Do you want to show her or should I" the future doctor asked his past

"Nah be my guest" the Current doctor said with a calm voice "oh did you bring it?" and upon asked the future doctor brought out a leather watch looking thing and pressed a couple of buttons "see you when I'm you" and with one final press the current Doctor vanished leaving the future Doctor in his place and it was clear that the doctor didn't vanish in smoke or magical energy in fact it seemed electrical and a smoke mark was left in his place

"Hello future me or I'm present me now, oh and Trixie here" the now current Doctor gave Trixie a pile of photos which were in fact foal pictures of different ponies including herself and each picture had the doctor in it even Celestia was in the collection as the multicoloured mane was uncanny

"how is that possible, you can't still be the same taking these photos you should be old" she stated dropping the photos revealing them to the crowd, but the doctor picked up the Celestia one as she would appreciate her Foal photo in the paper

"Time travel, you should try it sometime" seeing as she couldn't top that she resorted to a different tactic and did a similar bind to the doctor that she did to Apple

"Seems even you can't beat me even with your impressive talents" but the doctor was back on his feat quicker than she seemed possible

"met Houdini learnt his tricks, binds are like cake" and for some reason the Doctor was now wearing a Fedora which some of the mares screamed as he looked rather dashing and Trixie was losing her edge "here let me take your cape" flinging a small pellet to the ground the entire stage was in smoke and once it cleared there were 3 Doctors all wearing a tartan tie and different hats on with a fedora, one with a top hat and one wearing a fez and all three were holding Her cape which she still had on

"How is, how is there three of you!" Trixie was now a bit dizzy as even she couldn't comprehend how three could appear and be completely identical "triplets? It has to be!" but her theories where shot as yet another Doctor appeared from the crowd

"Sorry Trixie, I don't have any brothers, I do have sisters though" and again another

"Hey! So do I!" and one by one, more and more doctors showed up all with their eyes on Trixie who was more nervous than Fluttershy on a bad day. And one stepped forward wearing a tartan bowtie and sporting a smashing moustache

"Great and powerful Trixie! Meet your defeat at the hands of Doctor Rassilon! muhahaha!" but his one was shot down by the fedora wearing Doctor with a baseball bat

"You weren't suppose to show up, you old coot now scat" Doctor Rassilon sulking away and the Fedora Doctor turned to face his opponent "it seems I win" now completely freaked Trixie backed off afraid of the Time lord, Twilight did a quick count and saw 24 Doctors in all "see, even you can be stopped in your tracks and I didn't use an spark of magic, in fact most of your tricks are just for show, like what you did to Rarity, just a combo of green hair spray and some mud, and it's not difficult to spin rainbow out of control she does that enough herself"

"Yea, wait what?" Rainbow a bit confused at The Doctors statements

"but this is magic" taking of his hat and his Sonic screwdriver her tapped his hat three times and pulled out Spike (how he got there no one knew), Gummy (Pinkies pet alligator) and then he struggled to get the last one out, he hit his hat a couple of times even letting one of his other self's try but eventually to the surprise of every one, Trixie especially and the person who came out of the hat was in fact princess Celestia

"oh heavens, where am I" looking around she saw her student Twilight and her friends along with the rest of ponyville which had bowed after about two minutes of shock, finally looking behind her she saw the legion of Doctors "oh hello Doc…tors, do you mind explaining to me what just happened?" after asking her question The Doctor gave a bow (in the thank you kind of sense)

"Princess, a magician must never reveal his secrets, now back to canterlot with you" placing the fedora on Celestia's head and tapping it with his screwdriver three times again the princess was warped back into the hat with the Doctor replacing it on his head "ta da"

Now defeated, Trixie backed off "you may have defeated me Doctor, but you haven't seen the last of THE GREAT AND POWERFUL TRIXIE" flinging a smoke pellet, not at the same strength, to the floor Trixie could be seen fleeing and faint in the back ground was the sound of her vowing her revenge followed by screaming

"and my work her is done" with the entire crowd cheering thinking it was special effects every doctor used the same device the first one used and zapped out of existence. The mane six where proud and astonished at the skill of their friend, but like all magicians he had one last trick up his sleeve

"That was amazing, don't you think Twi!" sitting next to Twilight and eating popcorn was The Doctor with no hat or moustache and Gummy with his jaws snapped to his mane but realising that he was there the whole time made everyone jump

"How in the hay did you do all that?" Apple jack asked the grey Pegasus of time still eating popcorn

"I remembered I still had this vortex manipulator in my room, so by using the power of probability I decided to get it later on and give it to myself in the past while in the process visited myself over 20 times" he said showing off the device "I wouldn't of done anything but what she did to you three was just plain cruel so I had to reveal her flaws. Oh and pinkie this little guys yours" he said giving Gummy back to pinkie who jumped off in excitement but The Doctor had one more thing to take care of "Twilight right now I should be back at the house but I need you to give me number 25" rearranging his tie to a bowtie Twilight giggled and gave The Doctor a moustache turning him into Doctor Rassilon and using his Vortex manipulator he vanished

**BACK AT TWILIGHTS HOUSE**

In a flash of light the Doctor walked through the door to catch Twilight writing a letter to Celestia and spike with his own moustache sulking about a failed attempt to woo Rarity

"you're late you know!" Twilight said with a mischievous smile on her face and in a second the doctors fine moustache had become a large white beard as punishment for his lateness, but as Twilight learned that day, never ever give the Doctor Facial hair

_(Blue pointy hat appears on The Doctor head and a staff in his right hand)_

"A Time Lord is never late not is he early, he arrives precisely when he means to" making both his Companions laugh uncontrollably

**Next time on DW: EQUESTRIAN CRHONICLES**

**Longest night ever, The Grand Galloping Gala has arrived**

Courier: now, now, don't worry if you weren't satisfied, if you have seen the show a more epic battle will boil between these too foes , but for now back to the Story arc!

Doctor: Can I tell them? Can I? Can i?

Courier: no! _**"Reveals baseball bat of omega"**_(a most powerful weapon which can only be wielded by god himself of this world 'by Princess Celestia') BATTER UP!

Doctor: DOCTOR WHO IS BALSTING OFF AGAIN!

Courier what he was trying to say was that Episode five will and I stress the WILL involve _**"in a godly voice, complete with lightning and thunder**_" TIME TRAVEL!

So guess what the episode will be like, I may have left a clue in any of the chapters, as by the time I've written this I'll go to sleep with it on my mind.


	6. Episode 5

Courier: finally I finished it, this one took a bit longer since most of it is completely original and this is more or less a teaser for part two which is a glimpse into the future I hope for which, hope you enjoy it

Doctor Who:

Equestrian Chronicles

**Ep 05**

**Part one**

_The longest night: the shadow of the future_

**Black Hole Prison (The most secure prison in Equestria)**

Far in the future, by request of a certain hero a prison was built to contain the most dangerous criminals, but even after 300 years only 12 prisoners were ever sentenced here, one was so familiar it reminded the inmates of who built this hell

"Well, well, well look who we have here" a black Pegasus stood in front of the cell of the most dangerous Criminal in Equestrian history, the criminal in question was a Pegasus but he hid in the light so all the black Pegasus could see was the scar on his left eye accompanied with the hatred that kept him alive for the entire live of the prison he was in, he was Prisoner Zero

"What do you want" he said in a voice that would cause the prison to go berserk if they heard him on the bottom floor

"I want to make you a deal, i want you to help me remove your doppelganger from the picture, permanently" the Dark Pegasus stood with elegance and might and spoke with a cold but calm voice

"HA! He is no doubt the most powerful being in this s*** hole of a world" Zero laughed manically as the dark Pegasus knew he needed convincing

"Yes but he isn't the most powerful, that goes to his daughter" the news shocked Zero as he knew very little about the outside world the past 300 years

"A daughter!? I thought time lords were sterile"

"He solved the problem years ago, the wedding you attempted to use to ruin his live just fuelled his love for the bride, they have had two children a son and daughter, both extremely powerful, but the girl was born an alicorn and has enough magical energy that her power is equivalent to the Elements of harmony, hence her name" now informed about the family Zeros nemesis has made he wondered what this mysterious Stallion had in mind

"What's in it for me? Freedom won't do it i only have one live left and i will need to regenerate to stand a chance and i can't risk losing if i can't survive because he WILL kill me if he finds out who i am" Zero asked and explained while standing

"I can give you a new cycle, and the means to take him out, so do we have a deal?" the dark Pegasus asked with a smirk on his face

"Two conditions, how do i take him down and who are you?" unlocking the cell freeing Zero, the dark Pegasus walked away from the cell heading for a black box which looked like an elevator, standing next to the box was a beautiful grey earth pony with black hair,opening the door to the black box revealed a large room just out of Zeros view "a TARDIS!"

"How you take him out i'll leave to your discretion as for my identity you can call me The Valeyard" as he said his words the box doors slid shut and the Black TARDIS disappeared like all the rest but its sound was broken like it was as twisted as its pilot but on the floor was a note and a watch like device, the note read

_Don't look for me, ill find you, Professor_

_ The Valeyard_

"Well then, its time to pay a visit to my Doctor"

**PRESENT DAY, ONBOARD THE TARDIS**

They mane six where currently at rarity's to get ready for the Gala, The Doctor told them he would meet them there as he was taking the TARDIS, he was currently in his wardrobe trying on the TARDIS blue suit Rarity had made for him, even the TARDIS made the Pockets bigger, he was looking at him self in the mirror

"I look like my father just missing the spiky hair and the brown coat" after ogling himself he walked back to the console room and set the controls to Canterlot

VWROP, VWROP, VWROP

**CANTERLOT CASTLE**

As the TARDIS landed near the Canterlot gate, The Doctor stepped out in his dashing suit turning the heads of a few mares, reaching the main gate two guards stood to check tickets

"Excuse me sir but unless you have a VIP ticket you'll have to wait in line" looking as the guard with a smirk on his face he pulled out his Gala ticket which was signed by Celestia herself "my apologies sir i had no idea"

"No worries my good man just doing your job, here is a little something" giving the guard a gem he passed him and into the palace to look around, after a good sweep of the ground floor he came to the grand stair case with Celestia and Twilight greeting the guests that came to the gala

"Doctor!" Twilight greeted The Doctor as he walked up the stairs

"I am glad you could make it Doctor, Luna will be glad to have a friend to spend the night with" Celestia said with her usual elegance

"Well i got to say and no offence it looks pretty boring, please Celestia let be arrange things next year" Celestia gave a small giggle and nodded in confirmation "of course Luna is in her room" she raised her hoof to signal a guard, who in fact was a white unicorn with a blue mane similar style to Twilight's, it was her brother Shining Armour

"Hi Twily" he greeted his sister first as he had not seen her since she moved to ponyville

"Shining Armour, its great to see you BBBFF" of course the phrase BBBFF stumped The Doctor making Twilight role her eyes at her best friend "Big Brother Best Friend Forever" she explained

"Oh, fair enough, nice to meet you Shining Armour" The Doctor greeted the captain of the royal guard him giving a nod and turning his attention to Celestia

"Princess what is it you require?" he asked the princess, in a casual manner, most soldiers no matter what rank would address royalty with the upmost respect but this captain was calm and relaxed this as another example of Celestia's rule, she ruled with care and kindness

"I would like you to escort The Doctor to meet my sister" according to Twilight she never gave an actual order, instead she asked more often but ether because she is so kind and polite or because of her position no one will say no, even if they did she would forgive them and sort the issue out

"Of course Princess, Princess Luna's Room is this way" he addressed The Doctor and both left the presence of the Princess and her gifted student "bye Twily, i'll see you soon" Shining armour waved good bye to his little sister before walking off

"Remember to have fun Twi, but don't do anything i would do...in fact i should of told that to pinkie but oh well" The Doctor also said goodbye to his dear friend as her only brother escorted him to the reason he came here in the first place

"Bye you guys, and i will, see you soon BBBFF and don't cause a stir Doctor" Twilight said as both Pegasus and Unicorn left the main hall

**CANTERLOT CASTLE CORRIDORS**

As both stallions walked the halls, Shining Armour was thinking about this colt that he had to escort

"_Who is this guy, Twilight has never mentioned him unlike her other friends, the way he talked to her, it was almost like the way we talk to each other, this pony better not be involved with by sister in any way other than friends"_ shining was being the cliché Brother, concerned for the female friends his sister makes "so how did you meet my sister?" Shining asked trying to get as much info as he could about the grey coated Pegasus

"Its a long story, but to dull it down in the shortest sense, i crashed in to her house and eve since she was kind enough to let me stay" that was the most odd way a guy ever met a girl making shining eyes widen

"So Mr Armour was Twi always as paranoid as the way i know ..." before he could finish his sentence Shining pulled out his Sword and pointed it at The Doctor who just stared at it and back to Shining like it was a normal occurrence

"Let me get something straight, you better not have any funny ideas about my sister and if you ever hurt her in any way i will hunt you down and kill you my self" as both stallions stared at each other for what seemed like hours, The Doctor raised his hoof to lower Shining's sword

"Listen Shining, i do not like your sister in that sense, i am a lot older than i look so for me that would seem just wrong" he explained giving a shiver "plus in the time i've known her i see her the same way you do, as a sister and nothing more" now understanding where The Doctors loyalties lye, he sheathed his sword and turned around

"Ok, i trust you, but i stand by my word if you hurt her" he spoke with darkness in his voice, to which the loon of The Doctor gave a salute and both continued to walk to Luna's room _"i want to know why Luna wants to see him of all people, he's a complete nut, but Twily seems to trust him, so ill let it slide"_

Arriving at a large door marked with the symbol of the moon, Shining gave a small knock followed by a young female voice "enter" opening the door both shining and The Doctor saw Princess Luna at her window watching the moon and the party below

"Princess Luna, you have a visitor" turning her head to the door she saw The Doctor standing with a small smirk on his face, Luna was in her night form which made her mane longer and transparent like her sisters, it seemed that under the moon her power would replenish but decrease as the sun rose, Shining had seen her like this plenty of times before but the doctor only saw her like this once and she was asleep and ill at the time and the reaction was priceless

_*Pomf*_

It seemed that only The Doctor noticed it happening and he quickly brought his wings down but couldn't fold them

"_Bloody wings why are you being awkward now!" _he thought to himself with mental sweat pouring down his face

"DOCTOR! it is so wonderful to see thou could come" Luna shouted (no royal voice, still pretty loud) then she ran over to him and gave him a hug, returning the hug The Doctor saw Shining smirking trying hard not to burst out laughing and the doctor had no clue what Shining found so funny, till he saw one of his wings sticking up

"_Dam it wings!, i'm going to cut you off and feed you to a dragon" _The Doctors mental rage against his wings put his mind off Luna and his wings lowered, which made The Doctor think _"wait was i just aroused?...how odd"_ after Luna broke the hug The Doctor tried not to be distracted by the attraction he was having for Luna, an attraction he couldn't understand "its good to see you Luna, how have you been?" he said caringly

"Not much, in fact thy duties haven't really changed since i last performed them" Shining left the room closing the door behind him and letting the two chat each other to death

**TWO HOURS LATER (AND A LONG EXPLINATION)**

Both alicorn and Pegasus sat side by side on the balcony, enjoying the Night sky as both The Doctor and Luna's talents had some thing to do with the stars

"So thou change your appearance when thou are close to death?" The Doctor had just finished explaining where he came from and how he looks like he is and had just explained regeneration

"Yea, that's pretty much the jist of it, the thing is i don't know if it will happen next time, this world is so different, but i will probably still live my natural live span, so at least i can live knowing two of my friends won't die of old age" he explained everything in a cheery mood and Luna knew that it was all for show, she knew that the thought of this regeneration frightened him, living for 1000 years was bad enough but having to change your entire body, it must of been horrifying

"We never knew what it felt to outlive friends and loved ones, as we didn't have any" Luna was now depressed as she remembered her lonely childhood, her only friend being Celestia but after time had been to busy with her new royal duties to play with her

"Least you had a childhood, i joined the Time Lord academy at the age of eight and for the next ninety-two years i did nothing but learn, then after that the war started" Luna was again shocked that both had shared similar childhoods but he did not her the last part and before she could ask The Doctors spirit sparked once again "also what's with the thou and the we?" Luna was a bit confused as no one commented on the way she spoke before but then again she had only been back 4 month

"It is the royal we and this is how thy speakest" The Doctors eyes spoke for him and he knew something had to be done about that

"Well i think we need to twitch that i tiny bit" he said pulling out a Canterlot dictionary and Luna's eyes went wide with horror _"oh no, not school"_

**THREE HOURS LATER AND A UNWILLING STUDENT**

"Ok now repeat the sentence" the doctor said pointing a metal stick to a chalk board with some writing on it

"Hello my name is Luna and i am the Equestrian princess of the night, i have an older sister named Celestia... Doctor this is a Childs lesson, you don't have any reason to tell me how to speak, i don't even need it" Luna had sat on her bed listening to the doctor for three straight hours and she was sick of it

"Huzzah, not the sentence i made but you used modern words! And let me say from personal experience that speaking like you did just confuses people, but still your done" he said pressing a button on the chalk board which made it fold up to fit in The Doctors pocket, Luna on the other had was confused she was now speaking more modern and it was a strange experience for her

"Oh your right i am speaking like a normal pony, oh this is spectacular" she exclaimed with so much joy

"Well at least you have a large vocabulary" the doctor said with sweat dropping down his face as a reaction to Luna's excitement, then he felt a small vibration in his pocket "huh what the?" pulling out his psychic paper, it flashed in a bright blue light which drew Luna's attention

"Doctor, what is that?" Luna asked as she had never seen anything like The Doctors Psychic paper, in fact no pony has it was a human wallet after all

"it's called psychic paper, it allows the holder to fool the view to what they want to see, but it can also be used as sort of E-mail system" he spoke with precision and concern at the thought of who could send him a message on Psychic paper "probable my step mother"

"What's an E-mail?"After asking her question The Doctor snapped his head to face Luna, then her relaxed after realising Luna had been on the moon the past 1000 years and that the only computer he knew of was the TARDIS monitor.

"Uhh, who to explain, ahh you know how you send letters to people" he said hoping that she will get the idea.

"Yes, why do you ask?" she spoke slowly as it was common knowledge.

"Well it's like that but electronically, but never mind that now I need to read this" still unsure what the alien Pegasus was on about she walked behind him and while looking over his shoulder, read the note in his hand

_*We need help, come quickly_

_From Harmony*_

The Doctor looked up from the paper and directly at Luna, making her blush a bit since he was so close and both were in direct eye contact

"Do you know a Harmony by any chance?" he asked cocking his head, which Luna found adorable giving a small giggle given the near awkward moment, yet she didn't have to think very hard about his question

"My apologies Doctor I do not" she said sad she couldn't help him out, but The Doctor jumped up onto the table with his face full of determination and a sense of purpose

"Well then, we have no choice" he spoke with pride in his voice, Luna's heart was beating faster and she didn't know why

"_Why is it getting hot in here?, the window is wide open"_ The Doctor then leaped of the table and walked to the balcony ready to leap off the edge,

"DOCTOR STOP!" Luna would have tried to stop him but she had forgotten that he could fly but before he jumped he turned to Luna with a massive grin on his face and his eyes sparkling in her moon

"well come on then!" saying his words he fell backward off the balcony and soared of the Gala and realising that there was nothing better to do, she ran for the window and she too took off into her domain of the night sky. Look all over for the Time Lord Luna spotted him standing next to his Box once she landed she walked over to him slowly and she didn't look very happy "well that was fun wasn't it?"

"Doctor never do that you scared me to death!" she yelled whacking him on the head

"Oww! HEY!" complaining about the growing bump on his head the TARDIS door opened revealing the temple like room that resided inside and Luna nose up disapproval walked in first with The Doctor walking in after her

"so where are we going anyway?" she asked still annoyed at The Doctor who could feel her cold heart a mile and a day away

"well, a clever way to contact someone from the past is to send it to a place you know the receiver will be and the time they'll be there and this message is the opposite, it was sent from the future going back to point where the message was appropriate" he explained very quickly but like always he begins to ramble

"That does not answer my question" she said coldly and in the background the TARDIS made some noises which to The Doctor's surprise Luna seemed to like himself understand the old girl "huh? Who was that?"

"Wait you can hear her!" The Doctor said with shock in his voice

"Hear who?" now confused with what was going on around her, she never spent long in the control room only a brief few minutes

"The TARDIS, you can understand her!" he said with wonder as this has never happened before and along with his glee the TARDIS gave another series of sound which both The Doctor and Luna identified as a hello

"uhh, hello to you too…TARDIS, but any reason Doctor you still didn't answer my question" she asked once again

"ahh yes, well like a letter a psychic message has a sender and therefore an address" placing the psychic paper on what he called a scanner which resided under the keyboard below the monitor "coordinates set, ready Luna?"

"for what?" she asked with worry in her voice

"Adventure, AVANTI!" pulling a small leaver the entire room began to shake and the cylinder in the centre began to move, on the outside several ponies had gathered at the sighting of Princess Luna with a grey stallion, even Celestia and Twilight arrived to see what the commotion was about

"What is going on here?" Celestia spoke softly but at the same demanding, since she wasn't happy about rumors especially about her sister, one of the guard who arrived before Celestia walked over bowing to her before reporting the situation

"your highness, guards have reported seeing Princess Luna and a unknown Pegasus airborne and according to the public have both been seen here entering the box over there" he explained pointing in the direction of the 'box', Twilight looked over only to see the top have of what looked like the TARDIS

"but all I see is the TAR…DIS" she immediately realised that have the rumor where true as the other half was debatable as some said it was a kidnapping and other said it was Luna spending some time with that special somepony, but Twilight knew and didn't know of a way to explain it not only to her mentor but without the crowd hearing about the TARDIS, remembering The Doctors request from after the nightmare moon incident

"_Twilight, please do not under any circumstance tell anypony I don't know about my origins and the TARDIS" _The Doctor seemed pretty serious about it and Twilight knew what time travel could do in the wrong hooves so from that day on swore never to reveal the TARDIS or its owner to anypony including Celestia

"Every pony! I would like to put rumors to rest, my sister Luna is currently in her room preparing for the gala but was delayed due to her duties of guarding the night I can confirm this as I spoke with her before coming here, so please return to the gala and enjoy the rest of evening" knowing that Celestia was no liar the crowd began to disperse but as soon as they left a bright light shined in the night and the unmistakable sound of the TARDIS came to life and the Blue box disappeared but for some reason now pony noticed only Twilight and Celestia herself saw the disappearing act of the Time machine

"Princess, I can explain" Twilight had become even more paranoid at the clear fact of the TARDIS's existence

"No need my dear student; I know of The Doctor and his mastery of Time, it is why he called himself Time Keeper many years ago, I appointed him the royal keeper of time and the name stuck, oh I do hope Luna will have fun with him and I also hope she come back safe" Twilight was gobsmacked but she guessed that since The Doctor could travel in time he must of met Celestia at least once in the past but that was also his future, as Twilight tried to think this through she dismissed her thought and returned to the gala with her mentor

"Be careful Doctor"

**Next time on DW: EQUESTRIAN CHRONICLES**

**Sneak peak of the future DON'T blink or you'll miss it**

Courier: I had to think hard about this one as it sparks the relationship Luna and The Doctor have and I include several thing that I believe should have been include like Shining Armour, I mean it is possible he wasn't captain of the royal guard (though I doubt that since it was only one year before a canterlot wedding) but if I was that high up in rank wouldn't you stay as close to the monarch of the kingdom. So yea there you go

By the way I have made a video of my view and other things about MLP if you interested, plus if you have any questions for me or the story, you can look at my new Tumblr page, which needs some followers, I am thinking about making this an audio drama thing, as I have a form of animation. So please support these ideas, I would be so grateful

Any way have fun everyone, and remember to be happy!

**Tumblr: **

**Twitter: **** /TARDISCourier**

**YouTube: ****watch?v=r4QtudoxsAc**


	7. update (is about time)

hi everyone, sorry episode 7 is not done yet, i have had a severe case of writers block but by the time you have read this i will be working on it and all will make sense...By Doctor Who sense at least. so i ask you to be patient as i am trying to write every episode as a chapter each with some originals every now and then. thank you for your support and enjoyment in reading these episodes

with many thanks

Courier


	8. Prologue: 100 years later

Courier: since I have returned to the writers way I have made a prologue that will cover the background of the far future

Doctor Who:

Equestrian Chronicles

**Episode 6 part 2: prologue**

**Canterlot, 100 years in the future**

Canterlot one of the last strongholds for the Equestrian resistance, no one knew how the war started and no one knew how to end it.

Since the return of Princess Luna 100 years had passed, with the guardians of harmony, protecting the land but now most are gone, Rainbow Dash and Rarity are reported MIA and the power of harmony cannot be used unless all are together, pinkie broken by war (now going by Major-General Pinkamena) is in charge of the canterlot forces along with Commander Fluttershy (who had lost her shyness for the destruction of her home along with the death her animal friends).

Ponyville which was lead by Princess Twilight and Lieutenant-General Apple Jack, where the main attack force against the Dark forces.

The Doctor and Princess Luna where currently in the crystal Empire along with its rulers princess cadence and Field Marshal/Prince Shining Armour. During the first days of the war the Empire was the first to be attacked and thanks to some Time Lord Tech the empire became the safest place on Gaia. Yet everyone that swore to protect harmony had failed to do so for 10 years, Discord was the first to fall as he along with the mane 7 (plus doctor who is 7th) had engaged the dark forces but were defeated and discord was imprisoned in his stone prison by the leader of the Darkness The Professor. Most citizens hoped for Celestia to defeat the darkness but the High Princess, disappeared shortly before the war putting Luna in charge along with The Doctor but when they both addressed the public they said this war will be over in 10 years. 10 years have passed and that hope had vanished along with everything else.


	9. Episode 6 part 1

Courier: finally I finished it, this one took a bit longer since most of it is completely original and this is more or less a teaser for part two which is a glimpse into the future I hope for which, hope you enjoy it

Doctor Who:

Equestrian Chronicles

**Ep 05**

**Part one**

_Sneak peak of the future DON'T blink or you'll miss it_

**Canterlot Palace halls**

VWROP, VWROP, VWROP

As the sound of the TARDIS rung throughout the halls, the majestic blue box materialised and the door squeaked open with a young cheerful looking face popping out.

"Luna, we're here come on out" The Doctor walked out of the TARDIS now out of his suit, to avoid an angry Rarity and back with his trusty bag and tie, Luna also poked her head out to have a look around and slowly stepped out as this was her first time travelling through it. (Time I mean)

"Where are we, I'm sorry when are we" shaking her head to correct herself since she knew where she was but no idea when, The Doctor was looking at some rock which had fallen from the roof and also the shattered glass.

"About 100 years in the future, so I say the year 1100 precisely give or take a few decades" he said dropping the rocks and continuing through the halls.

"So what are we looking for" Luna asked wondering how her home got in this state.

"We're looking for a very powerful being named Harmony; the thing is I have no idea what she looks like" as The Doctor was telling Luna about their goal, the princess heard something move behind her and she turned to see several pegasi statues which looked like they were weeping lined up against the wall. "what is it?"

"Nothing, i thought I saw something move but I'll give you credit these statues definitely look old, me and Tia were talking about statues in the halls, looks like a won on that regard for pegasi" Luna looked at the statues with wonder as they looked beautiful but she didn't notice that The Doctor had frozen on the spot and his eyes wide with horror.

"Luna" he said very calmly but heavy with fear.

"Yes Doctor" hearing her Friends fear she turned to see him staring at the statue with horror on his face "oh please don't tell me your scared of some statues" giving a small laugh, but the Doctor was not in the mood to laugh.

"Look behind you" he stated not taking one eye off the statues.

"Look there is nothing to worry abo… Aaiiee" she gave a small scream to the statue which had moved clearly towards her and its face was full of bloodlust. "What in Equestria is going on!?"

"I've met their kind before, DO. NOT. BLINK!" as the two ponies stood back to back, The Doctor started to think of an escape plan. "ok here's what I've got, we could run back to the TARDIS… NO! Bad idea we would be killed before I could unlock the door, Luna can you see a door?"

"Yes" she replied shakily, scared for her life.

"Try and open it, but don't take your eyes of them, I'm guessing yours moved, so you're in more danger" Luna attempted to open the door but it was locked tight even her magic couldn't open it.

"It is locked, I could try a teleport" she inputted an escape plan but was quickly dismissed.

"No! we don't know a safe area in this time zone teleporting would ether land us in another group or attract them, so I wouldn't risk it" The Doctor continued to think and the only thing he could do was try to unlock the door himself but he then remembered it was made of wood. "god dam it, I bloody hate wood!"

"WHY! In all of Equestria would you complain about wood?" Luna shouted, not knowing the reason for her friend's hatred for wood.

"It's a long story, I'll explain later" then in a flash of light both The Doctor and Luna where surrounded by several ponies dressed in camouflage uniforms and all carrying a saddle that doubled as a weapons "WHOA!, hold it we come in peace!" it took the ponies a minute but when they saw who they were aiming at, their weapons folded away and each began to salute.

"Doctor what is going on?" Luna asked confused about the events that had transpired.

"Well it looks like they're saluting their princess" before The Doctor had answered a young voice had echoed though the room which was in fact the throne room yet it was in ruin. A couple of the soldiers moved away and in front of The Doctor and his latest companion was a young alicorn with pure white fur and a long flowing mane coloured gold and dark blue, surprisingly the exact shade of the TARDIS. As she walked towards the two time travellers The Doctor gazed at her bright blue eyes, only to be reminded of his mother.

"Who are you?" Luna asked as she too saw something familiar about this mare.

"Let me guess, Harmony" the young alicorn cocked her head not understanding why The Doctor needed to guess.

"yes, but you know who I am, I'm your…" just as the mare revealed as theHarmony that called for help a red blur shot down and knocked Harmony to the floor, after the crash a crimson red Pegasus was on top of harmony, which under normal circumstances for Luna, the entire royal guard would grab the assailant but the soldiers just shrugged it off just as they did when she used to crash into Celestia, like it was a normal occurrence.

"Harmony are you insane! You can't tell them that, they are the past versions of them!" as the red stallion who was a lot younger than Harmony shot a glance at both The Doctor and Luna. "see they look different"

"Fine! Fine!, get off Quantum" responding to the word the small pony got up and jumped of Harmony and sat next to her as she got up herself "I'm sorry, it seems you don't know us yet, I sent a message but it looks like it went to the past instead of the Crystal Empire" hearing this Luna felt a chill down her spine.

"You mean THE! Crystal Empire?" The Doctor looked at his new travel companion and wondered what this empire was as well as Luna's concern over it.

"Yes, many years ago before I was born the Empire reappeared and was retaken by the Guardians of Harmony" The Doctor knew who they where at least, he was the one who named the team of him and the girls.

"Any way you asked for help but from what if you don't mind me asking?" both the young stallion Quantum and Harmony looked at each other wondering if it was ok to say.

"I don't think it would be a good idea to tell you, this is your future after all" as she explained her concern a male voice roughly the same as The Doctor's in age spoke up.

"Unless they already know it" walking past several of the guards a unicorn with a Dark Blue coat walked slowly and with authority towards the four along with salutes from every soldier he passed.

"What do you mean Star?" Harmony asked.

"10 years ago those two said this war would end in 10 years. Obviously it wasn't due to our superior army as we are badly losing this war, unless they already knew the outcome" the stallion explained pointing accusingly at the two time travellers causing The Doctor to walk in front of Luna to respond to hostility.

"What is he doing?" Luna thought as she saw The Doctor walk in her path in a defensive manner.

"And who are you Blue Boy?" The Doctor asked with a slight anger in his voice.

"My name is Starlight Eclipse, captain of the royal guard and the Resistance, this is Harmony heir to the throne of Equestria and the small one is Quantum Knight both are my younger sister and brother" Luna noticed something that she found odd, it was his last name it seemed familiar.

"Wait! I am the only pony in Equestria with the name Eclipse!" it was puzzling for her as she did not understand yet The Doctor however could just see the resemblance.

"Yes, I understand you confusion but I see no harm in telling you. I am your eldest son which is why I bear the name Eclipse and these two are your only daughter and youngest" as Starlight revealed the truth Luna began to feel dizzy as The Doctor eyes widened in shock.

"Wow, I didn't see that coming" he then noticed Luna began to fall to the floor "Luna!" as Luna came to after fainting from the shock, the first thing she saw was the concerned face of The Doctor "you alright" gazing into his eyes for a few minutes Luna noticed that she was caught in his arms.

"Yea I'm fine but Doctor. You can put me down now" it took a second for him to process, when he realised the position he was in with her.

"Right! Right, I'm sorry" he said adding the red colour of his blood to his grey fur as he blushed, making both Harmony and Luna to giggle. As she got back up she stared at the three you claimed to be her children, she never thought she would even settle down due to her royal duties, she never got any sleep. Yet the most important question running though her mind was who the father was?

"Well, that was a shock, at least I don't need to think of names then" Luna said trying to lift the mood as the level of awkwardness rose.

"Any way back to business, what happened here?" agreeing to discuss this matter another time the four ponies began to discuss the events that have happened in the past century.

"10 years ago, a dark castle rose from the desert followed by a tide of changelings, this army attacked every major city it could find starting with the crystal Empire, yet you had added defences to protect it from invasion and Shining armour used his protective spell on canterlot, harmony is using her magic to power the shield however it isn't perfect, we are safe from air attack but the entire city is overrun by ground forces like the statues in the hallways and ponyville is the front lines constantly under attack" as Starlight finished explaining using his magic to create a visual PowerPoint of the events, both the doctor and Luna where shocked that any attack had gone this far.

"What about the elements?" Luna asked confused at everything that her future child had explained.

"The guardians of harmony engaged the main force of the darkness without the elements but in the first ten minutes two of the group where defeated presumed dead both where Rainbow Dash and Rarity" The Doctor was now dead inside he was there and he let two of his best friends die, his anger was boiling ready to take down the source of his pain.

"Who is the main force?" The Doctor asked only to be given the name of the one person or monster that he never wished to her till he saw his own grave.

"His name is The Professor" as Harmony revealed the name The Doctors hearts stopped.

"No…that's not possible" he said quietly as he remembered one of the worst nights of his life.

**Many years ago**

"_WHY! WHY WOULD YOU DO THIS! This isn't us, this isn't you WHAT ABOUT THE PROMISE, DOESN'T IT MEAN NOTHING TO YOU!, DOCTOR! ANSWER ME GOD DAM IT!" The Doctor (human form) cried over a young girl who was bleeding heavily and was clearly dead, in front of him was another, another Doctor holding a blood stained knife and a look on his face that showed the pain The Doctor had suffered over and over again and he had enough and it was time for blood._

"_hmm, I haven't forgotten it, but yet I don't give a dam about it, YOU WANT TO CONTINUE TO UPHOLD THE LAWS OF THOSE BASTARDS I CALL MY KIND FINE! BUT WHAT I DID IS A SMALL TASTE OF WHAT THEY TOOK FROM ME!" both Doctors kept eye contact one mourning the loss of his friend the other happy to cause the pain "never call me The Doctor again, I like Professor much better"_

**Present**

The doctors eyes where now cold with sorrow and anger, causing Luna to be concerned.

"Doctor? Are you ok?" as he lifted his head Starlight took a step back, he knew to fear the Doctor when he was in this level of anger yet never witnessing it firsthand.

"you tell me exactly where this castle is so I can pay myself a visit" The Doctor walked towards the wall as his cold eyes lay on the sword hung on the wall, ready to for the first time in 100 years…TO KILL.

**Next time on DW: EQUESTRIAN CHRONICLES**

Courier: well that to a while sorry for the massive wait, but I couldn't find a way for the old ideas to flow so I rewrote it and I'm proud of it this does mean there will be a third part or the actual part two depending on your perspective, but thought out the story I will try and explain the back-story between The Doctor and The Professor, mainly since I won't be writing the original adventure as humans before Doc met the pony gang.

Any way remember I am answering questions about the characters in any form on my Tumblr page and in time maybe a visual version of the story also there is my Twitter page and YouTube channel if you with to have a look

Thank you for reading and enjoy.

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**Twitter: **** /TARDISCourier**

**YouTube: **** watch?v=r4QtudoxsAc**


	10. Episode 6 part 2

Courier: finally I finished it, this one took a bit longer since most of it is completely original and this is more or less a teaser for part two which is a glimpse into the future I hope for which, hope you enjoy it

Doctor Who:

Equestrian Chronicles

**Ep 05**

**Part Two**

_FEAR THE PINK MIST_

**Previously on Doctor Who: Equestrian Chronicles**

"Where are we, I'm sorry when are we" Luna asked shaking her head to correct herself since she knew where she was but no idea when.

"About 100 years in the future, so I say the year 1100 precisely give or take a few decades" he said answering her question.

"So what are we looking for" Luna asked wondering how her home got in this state.

"We're looking for a very powerful being named Harmony; the thing is I have no idea what she looks like"

"The guardians of harmony engaged the main force of the darkness without the elements but in the first ten minutes two of the group where defeated presumed dead both where Rainbow Dash and Rarity" The Doctor was now dead inside he was there and he let two of his best friends die, his anger was boiling ready to take down the source of his pain.

"Who is the main force?" The Doctor asked only to be given the name of the one person or monster that he never wished to her till he saw his own grave.

"His name is The Professor" as Harmony revealed the name The Doctors hearts stopped.

"No…that's not possible" he said quietly as he remembered one of the worst nights of his life.

The doctors eyes where now cold with sorrow and anger, causing Luna to be concerned.

"Doctor? Are you ok?" as he lifted his head Starlight took a step back, he knew to fear the Doctor when he was in this level of anger yet never witnessing it firsthand.

"you tell me exactly where this castle is so I can pay myself a visit" The Doctor walked towards the wall as his cold eyes lay on the sword hung on the wall, ready to for the first time in 100 years…TO KILL.

**Continuation**

"Are you seriously thinking going there? No offence but the last time you where there you almost died and that was the future you!" Starlight was now trying to convince The Doctor to stop and think as he was on a blood fuelled rage that Luna, Harmony and Quantum could not understand.

"WELL YOU SAID IT YOURSELF, HOW COULD I KNOW IF THE WAR WOULD END IN 10 YEARS UNLESS I KNEW THE OUT COME, MAYBE I LOST THEN BECAUSE IT WAS A FIXED POINT, WHAT EVER THE CASE IS, I DON'T GIVE A DAM, THAT MONSTER IS GOING TO DIE AND IM GOING TO BE THE ONE TO CHOP OF HIS DAM HEAD!" his eyes know red with rage he had flown up and removed a sword from its stand hung on the wall "Luna, is ok if I borrow this" he asked now lowering his voice trying his best to calm down.

"Yes you may, but I must protest you said yourself one time that there is no need to harm if there is another way, is killing this person really going to return everything to the way it was, wouldn't be better to imprison him and make him stand trial for his crimes" Luna was clueless as to how The Doctor knew this Professor and why he had such a drive to kill him.

"I'm afraid that would do much" Starlight had strapped on his combat saddle and sheathed his own sword ready for combat.

"What do you mean by that?" Luna asked her Eldest as he prepared for battle.

"This is not the first time The Professor has appeared in fact his last appearance, he was stopped and sentence to death by age and for a Time Lord that is a long time" as Harmony explained that The Professor was already guilty of crimes that earned him a Death sentence, the first in her memory, she had recognized the Name Time Lord.

"Time Lord? But Doctor isn't that you're…" The Doctor turned around still with cold eyes and looked at the night blue mare.

"yes he is, but it goes a lot deeper than that, he is what I never became" The doctor took a piece of paper out of his tie and opened it up to reveal a photo, he placed it on the table which was set up in the middle of the throne room and What Luna saw made little sense, it was a picture of two People that where obviously not ponies, A young man wearing a black leather jacket and a Tartan tie which along with the style and colour of his hair matched The Doctor making Luna guess that is what he looked like before he arrived in Equestria, next to him was a young girl with long blonde hair and wearing a light blue sweater both had a large smile on their face as they had taken a photo in front of what looked like the Eiffel Tower in Prance "the Professor is from another universe but he jumped to mind to escape his own fate which was decided by the Time Lords, once he met me he found out that the Time Lords where gone, Destroyed in the Time war and so he decided he should exact revenge on the universe, that my people worked hard to protect for 100 billion years. I stopped him but at a price, that girl in the picture was the last friend I brought onboard the TARDIS and he killed her in cold blood and since that day I vowed on my own grave that I would be the last thing he would ever see" The Doctor took back the picture and returned it to the slot in his tie "after the Nightmare Moon incident, I saw that my coming here would allow me to make a new life and live peacefully but no, HE HAD FOLLOWED ME! HE WILL PAY FOR THE LIVES HE HAS TAKEN AND STEPPED ON, WITH HIS BLOOD!" The Doctors bloodlust reaching the point of insanity Luna had heard the story and was prepared to fight this battle along with her best friend.

"Then I will fight alongside you, this is my kingdom and no matter when I am from it is my duty to protect Equestria from hostile forces" Luna said placing a hoof on The Doctors shoulder as he stared out into the fallout of the 10 year long war.

"I will make my way to the Crystal Empire to inform both your future selves, so they can prepare to fight back following your lead" before he prepared to leave he looked back to Luna who spotted him glancing at her.

"Is something wrong Starlight" Luna said slightly worried.

"Nothing Mother, it's just its been so long since you had your hair like that I forgot how it looked" as tears began to fill her eyes Luna walked over to the throne and pressed a small button and following a secret compartment rose from the floor revealing two spaces for armour yet one was missing, the one remaining was a black armour which was covered in battle scars and looked like it fought in an incredible battle.

"Is that yours?" The Doctor asked as he examined the battle damaged set of armour.

"indeed, it was the very set of armour that I wore during the fall of the Crystal Empire over 1000 years ago…" as Luna moved towards her old armour the other space which was disturbingly empty rose some questions in Luna's head "Starlight I wish to know, where is my sister?"

**Castle of Darkness**

In the middle of the desert a black castle stood surrounded by changelings and covered in angles, inside the throne room of this grand castle sat an olive coloured unicorn reading a book, a Pegasus with bat like wings appeared and bowed before the unicorn.

"My lord, you called for the prisoner" after catching the unicorns attention he placed a bookmark in his book and put it down while several changelings dragged a white wounded pony in front of the unicorn. Unlike most ponies he sat relatively like a human and as he got up from his throne he walked down on his hind legs alone and when he was within reaching distance of the prisoner he swiped the bag from over her head to reveal.

"High Princess Celestia so good of you to visit, how long has it been since your last beating" with the bag removed the wounds that the princess suffered looked far worse than they did earlier, it was also apparent that her mane had been cut very short and the majestic rainbow colour it had had faded into a blood stained pink.

"Professor, when will you end this madness?" the unicorn revealed as the Professor gave a small chuckle as Celestia struggled to lift her head.

"You know that reminds me of a film from a small backwater planet I know of, but really I will stop as soon as The Doctor is dead or better yet bowing at my feet. But no, he continues to resist and prevent me from taking the Empire but what shocks me the most is that he hasn't attempted a rescue" he replied whole walking around the battered monarch before sitting back on his throne.

"He does not need to, he knows that you will fail just as every other has before you" this was followed by a maniacal laugh along with a hard kick in the face from The Professor.

"Hahaha, but did any of the others last TEN WHOLE YEARS! Yes there was Discord but look at him now, reduced to a hat rack" pointing at the statue of discord in a protective stance as well as being covered in hats "the guardians of harmony are powerless, canterlot is in ruin and you can't do anything to stop me" despite knowing it would only lead to pain when The Professor came close to Celestia's face she spat right in his eye, followed by a quick slap "bloody bitch!, TAKE HER BACK TO HER CELL! And give her an hour long torture session to liven her up a bit" the Pegasus that brought in the prison bowed once again to his master.

"Yes my lord, TAKE HER AWAY!" replacing the bag onto of her head, the changelings tugged at the chains imprisoning Celestia and began dragging her back to the dark cell she has known as hell for the past ten years.

**Canterlot palace**

"So not only is this a take back, it's also a rescue mission" The Doctor had put on a set of armour that Harmony had given him and Luna was also suited up ready for war.

"Yes, but we have had no intelligence or evidence to confirm that she is there" Starlight was going to alert the future versions of The Doctor and Luna but thought it best to brief them on the area they had to fight though.

"She'll be there, knowing him he likes to cause pain on others especially prisoners, my only concern is if she could survive 10 years of tortured, unless she knew something he wanted to know, then he would beat her till near death then prevent it so she could be interrogate again" the thought of her sister in pain for so long was disturbing but she knew she would not give up so easily.

"I hope your right, anyway to get to the desert you will need to go around ponyville…" The Doctor held up a wing to object Starlight's idea.

"Wait if we are going to have a chance at beating The Professor we will need the elements" this made Starlight a bit uneasy as he did not want to tell him.

"That's not going to be possible" he said with regret in his voice.

"Why not, you're the one who said that Rainbow and Rarity where MIA so if we pack the elements we can put a end to this quickly" he said still with a slight anger in his voice.

"The only issue is that the elements have been missing for decades and they won't work, both General Pinkamena and Commander Fluttershy have changed due to the war, you may get Fluttershy as she only seems to have lost her shyness but I'm afraid even Pinkamena is beyond even our help, she hasn't laughed since…" expecting The Doctor to complain he held up his wing as to say he understood, this was not the same Doctor This was a warrior.

"That's is not important, ether way we need at least the guardians if we are to have even a fighting chance" seeing The Doctors point he placed a map on the table and rolled it out.

"In that case we can send the General a message to gather for an emergency meeting on the train to ponyville, normally she would refuse but if you both sign the notice she won't have a choice the Commander will most likely attend with her. Then you just explain the situation and she should join you" it was a lot to take in as Luna was struggling to keep up, normally she was the one giving orders.

"_Now I know how the men felt during the fight against Sombra" _Luna thought to herself as she listened in.

"Then once you get to ponyville you will find Twilight in her palace…" then the bright side of The Doctor emerged yet only for a second.

"Whoa, whoa, whoa, hold it, I know see likes that tree of hers but it's no palace" unsure of what to tell both of them Starlight decided to avoid that topic.

"uhh, spoilers?" he said with a cheesy grin followed by The Doctor eyebrow lifting to show he was not amused "anyway, once you meet up with Twilight it will be just a simple charge to the castle, once I alert both of you at the Empire, I will try to send reinforcements" with a small nod from The Doctor, Starlight's horn lit up and he began a teleportation spell "good luck" Starlight wishing The Doctor and his mother luck before he zapped himself to his new location.

"What now?" Luna asked sheathing her sword after polishing it during the briefing, with The Doctor giving her a look she recognized from her father

"Now we move" following The Doctors words she began a teleportation spell of her own, inbound to the train station.

**Canterlot Station**

Since original equestrian weapons were ineffective against hoards of changelings The Doctor had reluctantly given the Canterlot army weapons similar in function to the very weapons he loathed, ballistic in nature it had turned most of Equestria into what he called Afghanistan. After receiving a notice signed by Princess Luna and The Doctor themselves, The main defence squad lead my General Pinkamena headed for the station only to be engaged by enemy forces moments after leaving the defence shield.

"What now, we are outnumbered and the General has pulled a Hoofdini on us" two soldiers had taken cover from the onslaught of the enemy behind the clock in the courtyard of the Train station after being ordered to scout the area, the one complaining was taking pot shots at the enemy to prevent the enemy advance and the other was bleeding from a magic blast to the leg.

"Stop your belly aching, remember The General always has a plan" upon those words the entire enemy line exploded followed by a lone figure that had jumped over the two soldiers and stood in front holding a massive cannon leaning on her shoulder in one hand and a SMG in the other, as several of the changelings recovered from the explosion along with others arriving, the figure standing on it hind legs lifted her head to reveal her pink fur under her black trench coat and equally pink straight hair along with the only part of her body which was not pink her piercing blue eyes "see what I mean" the soldier said before taking cover from the massacre about to take place.

"Let's party" seconds later both The Doctor and Luna had arrived outside the train station to see the entire courtyard covered in blood and standing in the middle was a pink mare wearing a blood stained trench coat.

"Pinkie is that you?" The Doctor said before the figure turned and threw a knife for The Doctor only just able to dodge it "Dam it Pinkie, you could of killed me" looking back to see the knife destroy a wall under the sheer force of the throw once he turned round he saw a 9mm pistol outfitted to her hoof so she could it correctly, aimed at his face.

"and I told you to stop calling be Pinkie" The Doctor was scared out of his mind he had no idea that Pinkie could be this dangerous but as the pink mare looked at his fore head she sheathed her weapon "Sorry Doc, didn't realise you where from the past but still don't call me Pinkie" the doctor gulped after coming inch away from death by one of his best friends, Luna was just confused about the whole situation.

"Pinkie, uhh I mean Pinkamena what happened here?" Luna asked as Pinkamena as she walked over to the two soldiers who were resting by the clock.

"We got a royal notice ordering both me and Fluttershy to met here, I guess that was from you" as she finished several pegasi and a chariot retrofitted for medical purposes arrived along with several soldiers and Fluttershy.

"Doctor! Ohh it is so good to see you!" Fluttershy had crashed into the Doctor giving him a hug, which was very unusual for her as pinkie signed some paper work to discharge the soldier for a medical leave.

"Fluttershy, you have changed usually you would barley say hello" Fluttershy was then pulled back by Pinkamena allowing The Doctor to get up.

"Commander this is The Doctor from the past, probably just after the Gala" both Luna and The Doctor where shocked they never knew Pinkie would even guess that.

"Ohh, well ether way I haven't seen you in a long time, it's nice to see you both again" there was a definite change in Fluttershy normally she wouldn't do half the things she just did unless she was furious.

"So what did you want us for and why didn't your present selves come instead?" pinkie had sat down on a rock waiting for the two to explain themselves.

"We are going to raid The Professors palace and end this war" according the Starlight, pinkie would of agreed in a heartbeat but instead proved him wrong.

"No" this shocked The Doctor and Luna as she was needed to end this 10 year old hell.

"What!" Luna exclaimed as she was about to lose her temper.

"Don't lose your temper over me princess, if you're from the past then you know the future so why didn't you end this before it could begin" Luna was going to knock some sense into the pink pony but decided against it hoping she would change her mind.

"I couldn't, that day, that first loss was a fixed point, I know future events if I change those then my reason for doing so disappears causing a paradox which I cannot allow, it would destroy everything" she never seemed it but Pinkie was very smart and she could understand where the Time Lord was coming from.

"Fine I will help but it's because I owe you quite a bit, if it where up to me I would rather die fighting" with both Pinkamena and Fluttershy both agreeing to help all four entered the train and it began to move towards Ponyville.

**Next time on DW: EQUESTRIAN CHRONICLES**

Courier: HOLY COW, I never thought I would be doing a three parter, but that's me not wanting to exceed 10 pages per episode but don't worry folks as next episode will give you Nightmares.

Thanks for reading an please comment on your thoughts it can only get better if you share your opinions

I also have a tumblr page where I can show images made on pony maker of OC characters and I will answer question regarding character backstories or forestories and certain plot points to get there simply type in Doctor Jr (as spelt) and you should find a blog with a pic of a grey Pegasus

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**Twitter: **** /TARDISCourier**

**YouTube: **** watch?v=r4QtudoxsAc**


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